Aaron Williams of Premiumbeat has written an excellent overview of how to prep Adobe After Effects for finishing:
I initially started doing it because I was creating videos for a specific non-standard aspect ratio being projected by a set of image blended projectors. All of my videos had to be cropped to 2048×768, and at the time I was editing in FCP7, so all of my videos had to be formatted for this aspect ratio in After Effects. I loved the power and flexibility of the workflow so much that I kept on doing it after we moved back to a standard 1920×1080. It became even easier when I moved to Premiere Pro as my primary NLE.
He offers 4 main tips:
1. Use placeholders for text
2. Keep tracks to a minimum and stay vertically organized in Premiere Pro
3. Use Dynamic Link but don’t trust it
4. Export an audio mixdown
Read the details of each tip and the entire workflow here.