Can I make my pixelated images in paint, import them piece by piece into Moho, and then add bones? and make certain parts of the sprite not get distorted?
You should be able to do this by exporting from your paint program using the PNG. extension. There are tutorials explaining how to do the boning. I'm a noob so I don't know about distortion of sprites???
You can only prevent the entire image layer not to warp, not a part of it. This probably means that you should put the part that shouldn't be warped in a separate image layer and it may involve additional preparation (more and overlapping image files). In the image tab of an image layer you will find a check-box to manipulate the warping of the image layer.
And remember that Bone Strength can help to have some control over bones/images interaction, plus you can choose between two different ways of interaction too in Bones tab of Layer Settings window. You are free to play & experiment with all this