Is there a way to easily batch convert hundreds of video files to h.264, while retaining the original dimensions, metadata, etc.?

I am organizing my library of stock video footage so is easily view (show to clients) and access. I need advice for two things:
First: What is a good program to catalog footage in? I am considering using iTunes because I already have it and I could setup smart folders to easily organize footage.
Second: I would like to encode all the footage to h.264 so I can preview it in Quicktime and add it to an iTunes library. My problem is all the footage is in a wide variety of dimensions, formats, framerates, strange codecs etc. I have access to Adobe Media Encoder and Apple Compressor. Is there a way to easily batch convert hundreds of video files to h.264, while retaining the original dimensions, metadata, etc.?
I have tried using a watch folder in AME but it freezes every time I add the folder...
Thanks for any help!

"including library and music folders) from my computer"
Did you move the entire iTunes folder the hold Option, select Choose library and select the iTunes folder you moved?

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