And what specifically? I'm sorry to say so, but I really think you need to start from the beginning and learn the AE basics first. you sound massively confused about how AE actually works and what it is meant for. I'll wait for Todd to fill in more spoecific links, as his brain seems to have a built-in excel chart of each help page, but for starters read about trimming, splitting and placing layers on the timeline and also do have a look at the FAQ section of this forum.
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You shouldn't use AE to edit. It is not an editing program. I mean, you can edit in it; it's just not built for it. Just like you can cut a log with a spoon; it will just take a lot longer and you'll cry a lot more.
Here's a great set of resources put together for people who are new to AE that should start you off learning how to use it. Go through them all.
However, to answer your question: After Effects works very well with .MOV files, but how well it works with them depends on the codec used. AE CS5 seems to be able to handle all of the ones I've seen people try to use, but earlier versions had issues with certain types of footage and you haven't mentioned what version of AE you're using or what codec the MOV files are encoded as.
Thank you all for your advice and help. I only wanted to change some text in a video template that was created with the Adobe After Effects program. As you said it is proving to be more trouble than it is worth. I will go back to the drawing board so to speak and start from the begining Mean while I will just create a new video with another software. I do thank you very much for your input as it may have saved me hours of wasted time.