I'm using footage shot in 1080p on a Canon HV30. I captured the footage in Premiere as a Canon XF mpeg2 and am editing in a sequence with the same settings. I can't seem to find any settings for rendering this format in After Effects, though. Also, when I create a new comp using the Canon XF mpeg footage, it creates a 1440 comp rather than 1920 which is what the Canon XF 1080 sequence is.
So I guess what I'm wondering is what settings in After Effects work best for Canon footage? Is the Canon footage really 1920 or 1440? If there's no Canon preset in After Effects, should I be creating 1440 comps or 1920? Also, everything I've tried exporting (except for lossless) stutters when I bring it back into the Premiere sequence.
You don't typically created movies from After Effects in the same format that you brought in from you camera. There's a huge difference between acquisition formats (used by your camera) and post-production intermediate formats (as you usually put out from After Effects) and delivery formats (as you usually put out from Adobe Media Encoder or another compression application).
See this FAQ entry:
Regarding import and composition settings:
When you import a movie, you can then just drag the footage item to the New Composition icon at the bottom of the Project panel to create a composition with settings that match those of your movie. If you shot at 1080 vertical pixels, and the movie has 1440 horizontal pixels, those pixels are almost certainly meant to have a pixel aspect ratio (PAR) of 1.33333. If that's not how After Effects is interpreting the footage, then you can correct that in the Interpret Footage dialog box.