So you've just had this brilliant idea for an animation, and you're thinking: by Jove, I'll do it! Well, that's the spirit! But before diving in head first, I personally find that it's a good idea to take a deep breath, push aside the enthusiasm for a bit, and start drafting up a plan. It doesn't need to be a detailed screenplay at this point, but it helps if you can at least jot down some notes on the basic story/idea, followed by a rough shot-by-shot breakdown.
The synopsis is important in clarifying what you'll be trying to convey through your animation, and it's something to which you'll keep referring to as you prepare your shot-by-shot breakdown. If you are just one person trying to create an animated short, you'll quickly become aware of your own limitations (in terms of time, resources, skills, etc.); and as you do, it helps to go back to the synopsis and ask yourself: OK, if this is what I want to achieve, then what do I really need, and what can I cut or simplify because it might sound cool, but it is not ultimately necessary to the main idea.
The shot-by-shot breakdown, on the other hand, can be as complex as a sketched storyboard, or as simple as just a few words describing what each shot will show (not how, just what). I would suggest not trying to force yourself to start with storyboards if you're not comfortable with that; just choose whatever method is easiest at this point. There's always time to refine it later, and you really don't want to get bogged down right from the start.
So why do all this? The point is to give some shape to your initial idea by trying to imagine what it will actually look like. Not only will it help clarify your own ideas, but it will also help you in figuring out how to actually make it all happen.
Once you've figured out what you want to show, you can start figuring out how to go about it, based on what you would actually need. If you haven't yet decided on a particular animation style, your choice might well be influenced by the requirements which are starting to shape up. Try to keep in mind your limitations, and work around, rather than against them. You might be thinking of yourself as someone who can't draw, and as such have discarded the idea of hand-drawn animation, but if your story demands that you show a crowd, for example, that's probably not going to be feasibly achieved with puppets (alone). In such a case you may decide to either choose a completely different animation technique from the start, or else to complement your main technique with various others for individual shots (e.g. cutout animations, digital 2D or 3D, etc).
A Shroud of Silence was created mainly with stop motion puppet animation, but there is a fair bit of digital 2D used to complement it. Digital 2D has been used both to create new hand-drawn elements, and to manipulate and touch up the original puppet animations (adding tweens, fixing glitches, etc.). I will go into more details further on, but for now it helps to keep in mind that you should always keep your options open, and not limit yourself artificially. Making animation on your own is difficult enough as it is.