To add to what Victor said, you should definitely keep the Adobe Media Encoder!
I never use After Effects to compress my final video. Here’s Dave LaRonde to explain why:
Dave’s Stock Answer #3:
Don’t use AE to compress files for final delivery. The various compressors are there only to make quick ‘n dirty files showing a project’s progress to producers, clients, the kids, etc. AE is incapable of doing multipass encoding, a crucial feature that greatly improves the image quality of H.264 and MPEG-type files in particular.
Render a high-quality file from AE, and use a different application to do the compression. Popular ones are Adobe Media Encoder, Sorenson Squeeze and Apple’s Compressor, which comes bundled with Final Cut Suite. Even compressing in Quicktime Pro is better than compressing in AE.
– The Great Szalam
(The ‘Great’ stands for ‘Not So Great, in fact, Extremely Humble’)
No trees were harmed in the creation of this message, but several thousand electrons were mildly inconvenienced.