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Editing Workflow For iPhone 4

So i just got an OWLE Bubo for my iPhone 4 and have been taking a lot of video lately that I wanted to start editing.

I've figured out that I needed to transcode the H.264 video the iPhone 4 produces to something edit-friendly like ProRes 442. I've done this in Compressor and its all gone fine and well, but it still makes me render everything that I put in the timeline...

Is this because of the audio not having been transcoded as well? I cant seem to find any concrete info online that says you gotta convert it also...

Anyway, I tried to convert the original H.264 again and it makes two files...the ProRes 442 video file and an .aiff file. Is this correct? Am i going to have to sync up the seperate files for each clip before i can start editing any of them correctly?

Im pretty new to editing so this may sound stupid but any help would be appreciated.
 
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