No need for animation codec.
You need to get a grasp on how these programs operate.. If your sequence setting is that of a particular codec, such as pro res 422 or DVCPRO, then all media that is brought in to that sequence will be re-rendered/transcoded to match the sequence..
Again, I would avoid rendering out of AE to h.264 as it will take a ton of time to do so.. You would use Apple Pro Res 422, or 422 LT (differences are bit rate)
So you know, the animation codec is a lossless codec, it is nearly un-compressed, and for most situations completly overkill. If you are bringing in a video clip that is 1920x1080, h.264, with a bit rate of 25 mbp/s and adding some effects to it, then exporting to animation codec, you just blew that file up with a 200+ mbp/s bit rate.. and did it add any quality to it? NO... you just made the file larger then it should.
Do some tests to see what yields you the best results.