Are you asking how to prepare them for use in AE or what to render them when you render out of AE?
What are you trying to do with that footage in AE and what is your intended use for them after you render them out of AE?
Also, MOV is merely a container format, there are many different codecs that it could contain. Some are lossless and perfect for an intermediary file (such as the animation codec, PNG codec, etc.) and some are lossy (Sorensen 3, Photo-JPEG, etc.)
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i make some short clip with some effects and i want to render it out of AE. i just want to watch it on PC and maybe put it on web, but that is not primary. i try animation codec and quality is ok but everything got blue, like the blue channel is somehow increased. i don't know why.
Animation is usually the best looking of all the mov codecs. You should try H.264 for the web. Both of these are .mov files. As far as the blue that is probably something in your composition. Check for a layer or an effect you meant to turn off and may have forgotten. That is normally the case when I see a glitch in one of my renders.