Whenever I go from Illustrator to Flash I save in Illustrator as a .swf. Then in Flash I just use File --> Import and it pops up on my stage. In Illustrator when you export you have the option of exporting each layer as a separate frame in Flash so that way you can separate your artwork. Thankfully Flash has the Paste in Place option (oh how I wish Illustrator did!) so it’s easy to move things from separate frames onto one frame.
It sounds like you did this already yes? So what problems exactly are you having?
:bu:
:edit: It also helps to make sure you don’t have excessive anchor points on your vectors. In Illustrator you should try to simplify your paths as much as possible without ruining the lines before you export to swf. Then they will look better in Flash.