I agree that being more specific could probably get you better answers, but based on the info I've got:
Explode Shape Layers is the most helpful script I know for simplifying the Illustrator-to-AE workflow. It is a small dockable toolbar that helps automate a lot of the dissecting often required for imported Illustrator files with more than a few pieces.
Traditionally, separating everything onto its own layers in Illustrator was the way to go, but that's admittedly time-consuming and tedious. The "Create Shapes from Vector Layer" command (under the "Layer" menu) can now (as of a few updates ago) recognize distinct objects within an imported Illustrator layer, which is awesome, but with anything even mildly complex, you'll probably end up with dozens of paths on a single Shape Layer, which becomes unworkable pretty fast.
Explode Shape Layers has buttons that easily allow you to separate all those distinct objects into their own shape layers, or combine selected layers back into a single shape layer, as desired. It helps you get rid of empty paths, and can allow you to select all the fills or all the strokes on a shape layer at once.
While shape layers can be dense (and probably intimidating until you wrap your head around them), they give you a ton more control than you'd get by just importing layered-out Illustrator files.
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If I have a complex Illustrator file I need to animate, I typically do a mixture of the above. I'll plan out what I intend to do with the pieces of the artwork, and probably do some layering in Illustrator to separate things into appropriate groups. I'll import the whole thing as a composition, then convert some (sometimes all) of the layers into shape layers. If a piece doesn't need any internal movement, I'll often just keep it as an Illustrator layer for ease.
Also note that Illustrator text doesn't have the ability to be recognized as editable text in AE. If you've got a text-heavy Illustrator file, the best workflow I've found is to either copy/paste the text one at a time from Ill to AE, or to export your Illustrator file into a PSD. Open that in Ps, convert to RGB, send to AE, Layer > Convert to Editable Text.
Was that some of what you were looking for?
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