Okay, if I understand well your question…
Adobe After Effects shows transparency as a black color. So when you import a file, wheter it’s a picture [(below the size of the main comp for example, so you see black (tranparency) around)] or a video footage that you keyed and you see some black under it, that’s the transparency. Just do Composition > Make Movie > Output Module > Quicktime (any format…etc.) and be sure to render with RGB + Alpha.
Black = Alpha in a certain way.
If I didn’t answered your question, just tell me (or us).
Hope that helped.
Justin Productions
Tangerin01@hotmail.com
Adobe After Effects 6.0 Professional