I recommend rendering and exporting a losslessly encoded movie from After Effects and using a dedicated compression/encoding application to create the files for final delivery and distribution.
———————————————————————————————————
Todd Kopriva, Adobe Systems Incorporated
putting the ‘T’ back in ‘RTFM’ : After Effects Help on the Web
———————————————————————————————————
If a page of After Effects Help answers your question, please consider rating it. If you have a tip, technique, or link to share—or if there is something that you’d like to see added or improved—please leave a comment.