Um, I don't know of any codec that allows for a transparent component. Seeing as how there's no application that uses such a thing, it doesn't make a lot of sense.
If you're using After Effects and you want a bit of animated stuff (say, credits) to appear composited over some
other piece of animated stuff (say, Mel Gibson doing something unmentionable with Carrottop), then you just animate it that way.
If you must do it separately, then simply precompose the first bit.
So, to answer your first question, if you're producing titles in Photoshop, then you are producing still images of one sort or another. In Photoshop, just leave the background blank of your credit image and import that layer from the PSD. It'll be transparent.
If you must export to some kind of file, then export to a file type that supports alpha channels (for example, PCT files) and After Effects will assume the alpha channel is for transparency.
Cheers,
![[monkey] [monkey] [monkey]](/data/assets/smilies/monkey.gif)
Edward
"Cut a hole in the door. Hang a flap. Criminy, why didn't I think of this earlier?!" -- inventor of the cat door