I´ve been using After Effects CS4 for the last 5 months so I can say little about it.
I dont produce my footage in Maya, AutoCAD or ArchiCAD. I rather use Artlantis 3, but I think the logic for importing would still be the same. So here is what I do so far: I like to export my animation from Artlantis in frame sequences in JPG or TIFF format, usually in 15 FPS or higher. Then using this bunch of images I can build the secuence in After Effects.
Hope it helps.