I ended up using the capture program with the stand-alone MainConcept encoder, because it gave me the most consistent captures with no dropped frames (crucial for good IVTC.) Sony Vegas works great with my Fire wire camcorder (and keeps audio and video in sync), but it apparently doesn't like my third-party videocard drivers. Otherwise, I would use it for every thing.
As for running filters during capture - don't. You want your CPU focusing getting all that video in the best form possible. Save your editing/filtering for the resulting capture, when you can test without making anything permanent. The only filter I've run is the cropping filter, which actually cuts down the amount of video the program must capture, so that's a good thing.