Stumbled on some great tutorials that show you how to go about doing handdrawn animation in Flash, paint your lineart in flash and finally composite in aftereffects (add shadow, background and layering).
I did not create these tutorials, I am just sharing these because they are useful, for more info check out their website: http://base14.com/blog/
1) Handdrawn animation in Flash:
This is the exact same process I use for my animations (except that I am a better animator - I kid...not really :P)
2) Paint your Lineart in Flash
This is not how I work, I actually take an extra step where I clean up my lineart in Photoshop, and paint in Photoshop. But it's a nice tutorial nonetheless:
This was most useful to me, this is how to import your linework into Aftereffects, apply a shadow and use layering effects for extra depth.