At one point, I created some fills with the brush tool on separate layers,
overlapping, and some were transparent so the others showed through. Then I
converted them to a movie clip, and everything got put on one layer, yet it
retained the overlaps and transparency. Now if I go to edit the movie clip,
everything gets cropped so they no longer overlap. I'd like to split them up
onto layers (or just edit it) without that happening... is that possible? Does
anyone know how?

I'm not sure what you mean when you say everything gets cropped. I'm guessing
that when they got converted into the movieclip on one layer, the overlaps
became unique selectable entities in themselves... no longer transaprent pieces.

You would get what you want if you created the movieclip first (an empty one)
with sufficient empty layers added and then copied the timeline/layers of what
you drew into the new movieclip.