I usually cut in Premiere Pro. Then the smaller sections that require After Effects get copied from the Premiere Pro timeline to the After Effects timeline. I perform the task in AE and then export to the same exact codec I use in Premiere Pro. Which is either DV-AVI or the Cineform codec depending on if I am editing SD or HDV.
Why not use uncompressed? Because Premiere Pro is going to have to compress it anyway while rendering. So I might as well only render once – in AE. Since I do my titles in AE, there is little chance that rendering in Premiere Pro will be necessary if I bring it back in properly.
Steven
Adobe Premiere Pro 1.5.1 / After Effects 6.5 Pro https://www.stevengotz.com
Learning Adobe Premiere Pro 1.5 https://www.lynda.com
Contributing Writer, PeachPit Press, Visual QuickPro Guide, Premiere Pro 1.5