For me (and at any place I've worked,) it's all about planning first. This is what's known in the industry as preproduction. It's basically the part where you figure out the story, design all your assets, and it should be the only the time to explore story options. IMO, this is the most important part of production--without adequate preproduction, shows are likely to miss deadlines and/or run way-over budget. Good preproduction can also give you the confidence and energy to go from here to there...and, trust me, you're going to need it.
Assuming you have a concept in mind or maybe even a script ready, the next thing to do is create a storyboard and design the characters and environments. The order you do this in doesn't matter too much--in fact, it's often done concurrently. Personally, I like to do a quick design pass on the characters first so I have something to draw in the boards, and then I'll do the boards. After completing the boards, I'll focus on final character designs because the actions drawn in the boards can influence how it will be constructed and animated. You can hop back and forth of course, but I generally find it easier and more efficient to start and finish one task before moving on to the next.
Next comes editing the animatic. This is a version of your movie using images from the storyboard and an audio track. The audio can be a temp track (a.k.a., a scratch track,) which is used mainly for timing. Pay a lot of attention to this phase because you will be animating directly to the edit and it will be difficult, or at least very wasteful, to change your mind about it after you've already starting animation.
That said, don't go crazy with animating your animatics. Some animatics have limited animations but it's usually just sliding cut-outs from the boards, and camera pans and zooms. Any animation in an animatic only needs to be informative, not pretty.
You can see a few examples of storyboards and animatics that were created for personal shorts on our website. I'll try to get more examples up later this year, and maybe some boards I created for commercial productions and video game cinematics.
Once you're happy with that, it's time for production.
How you approach production depends on the style of animation you have in mind, and how much time you wish to spend on the project. BTW, it's good to set deadlines, otherwise you may never finish the project. Since this is your first Moho project, it's okay to be flexible until you develop a feel for how long things take to do. In fact, it's better to have a bunch of shorter deadlines to meet certain milestones rather than just one arbitrary end date. This way, you can see the actual progress your making and make adjustments to workflow methods and schedules along the way.
From here, I'll avoid going into too many workflow details because it will vary by users and animation styles, but here's 'checklist' of steps:
1. Decide if the characters are going to use vectors, bitmaps, or a hybrid of both. You also need to decide how the character will turn. (Smoothly, popping, something in-between, 90-degrees, 180-, 360? I recently rigged a character at work that had to smoothly turn 720 degrees, or 360 in either direction.) Also consider the motions required by your storyboard/animatic. Design the characters with that in mind. If something seems like it's going to be too complicated or difficult, now is the time to make the adjustment...and usually, this is easier to do in the storyboard/animatic. Now, design your characters with all this in mind.
2. If vectors, import the art to use as drawing or tracing reference. If bitmaps, segment and layer the artwork as necessary in your paint program. If you're using Photoshop, you might have to create a simplified version of the PSD to import, or can export the layers you wish to use as individual PNG's with transparent backgrounds. Then import the bitmap art. (Note that layered PSD support is a Pro-only feature. For Debut, you should use PNG's with transparent backgrounds. FYI, for various reasons, I prefer the latter even when working in Pro, but choose whichever is more efficient for you.
3. Obviously, you're going to need backgrounds. You can do them now or create these later. When I made Scareplane (my first Anime Studio short,) I asked my wife is she would paint the backgrounds for me. I gave her the animatic and a bunch of scale thumbnail sketches for her to work from. When I was animating my scenes, I used my thumbnails as background art and replaced these as she completed each painting. (Usually, I'll provide fairly loose sketches but I made these a little more specific because the characters had to interact with the environment so much. Looking back, I think I made this project more complicated than I should have for our first 2D film...see the note about 'first projects' below.)
4. Now you're ready to start rigging. I generally start with the basic skeleton. Once you have a good functioning skeleton in place, then you can work on Switch Layers, Smart Bone Actions and setting up Smart Bone Dials, and other details. Be sure to test your rig as you build it--it's easier to catch mistakes and fix problems as they are introduced.
Don't stress over getting the rig to do every possible thing under the sun...if you can get it to do at least 75% of the poses and motions, you're actually in good shape. If you can do more, that's better of course, but chances are that some really difficult poses and motions may only occur in one scene and may never be called for again. In those situations, it may be easier to setup a modified rig or a simpler 'one off' rig
to do just that one thing for the scene. Otherwise, if you try to build EVERYTHING into your rig, you may wind up with an unnecessarily complicated rig that may be difficult to animate for most scenes.
5. Before you start animating, it's good to create a shotlist. This is a list of all your scenes and information about each scene to help you set up and get the scenes finished quickly. This should include scene number, duration in frames (from the animatic), a brief description of the action, dialog and sound notes. If you have vfx or a special setup in mind, you might want to note that too. You can do this on paper or in a spreadsheet program like Google Spreadsheet or OpenOffice.org. I prefer the latter because I can use the spreadsheet to dynamically show me status and progress of the project. Also, if you use Google Drive or Dropbox, you can access your notes from any computer anywhere. (With Google Spreadsheet, you might want to take advantage of offline mode.)
6. On to animation.
When I'm working on my own productions, I tend to group all similar scenes together (like scenes that share the same backgrounds and environments,) and knock out each group in order of expected difficulty. This is because I'll gradually lose energy throughout the production so I want to save all the easy stuff for last.
Animation can be broken down into stages too.
First, I'll set up the scene(s). This means setting up the scene properties (resolution, frame rate, duration, etc.)--you can setup a template with your settings if one doesn't already exist. Then, import the environment art and your character rigs for the scene. You may wish to set them all up at once, or do them as you begin each scene...whichever works better for you. You'll then want to import the audio and frames from individually cut scenes from your animatic for reference. This will give you timing and placement info, and leave no questions about what you need to do to complete the scene.
When animating the character, I generally you first block out your poses to get the timing down, and then you go back and refine the animation. If I'm on a production for somebody else, I'll step-key the poses (i.e, all holds, no smooth animations,) and show that for approval before doing the actual animation. When the blocking has been approved, I'll change the keys to smooth, and the work on the animation. However, when I'm on my own projects, I won't bother with stepping--I'll just animate the keyposes straight through.
When I'm working on the actual animations, I'll do it in multiple passes. First, I'll get all the limbs and body animation done. Next, I'll work on faces and hands. Then, secondary animations, like hair, clothing, tail, wings, etc. Finally, I'll add subtle squash and stretch to the overall character--this can usually be done by simply transforming the group the rig belongs to. Be sure to place the group origin to a position that makes sense for the character (usually on the ground between the feet.)
7. Finally, render the animations, composite them if that's part of your workflow (I do this but it's optional,) and overcut the scenes to the corresponding scenes in your animatic edit. When you've overcut all your scenes with final animations, you have a finished movie! (Well, chances are you'll want to go back and tweak a few things but anyway you'll be almost done.)
Knowing what to do at each stage and far to take it comes with experience, and you should be careful not to overreach your experience level. I suggest developing a simple project first, something you're pretty confident you can finish. Whatever that project is, it will very likely turn out to be more difficult than you expected (it always is.) But when you pull it off, you'll be ready to move on to bigger and more ambitious projects.
Good luck! I'll look forward to seeing your Moho debut!