I use the two together all the time. Just for the record, Vegas WILL do a good percentage of what After Effects will do, although I find a bit of it easier in AE.
But, here's my workflow (using AE standard 5.0 & VV2)-- open whatever clips you need to mess with in AE. Save them as uncompressed files, then bring them into Vegas and add them into your project. Saving them as uncompressed may be time consuming, but I've had some video come out very, VERY badly when I've moved from codec to codec.
As for compatibility... what do you mean? Can you open AE within Vegas? Nope. Can you import AE projects into VV? Nope. But the workflow isn't any more difficult than you'd get with AE and anything else, either.