I guess when you say “smaller files” you have the ProRes files in mind. FCP works best with ProRes so you are totally correct to use that for editing.
Although the H264 files for instance, that your 5D produces are much smaller in size they are much more heavily compressed and H264 (and MPEG 4) are not good formats to edit with in FCP largely because they are not frame based codecs.
So when you transcode to ProRes you will always end up with a much larger file. You dont say which ProRes you are using but one thing you could do is use ProRes LT. That is a slightly lighter codec than 422 or HQ and is certainly sufficient to preserve the quality of the cameras you are using. You will find the file sizes slightly smaller if you do that.
You are using good quality cameras producing full HD images and thats always going to produce large file sizes. So in terms of your edit you are already using the optimum quality.
You can edit with H264 directly in PPro but there are still limitations with what it can handle so you may want to look at that especially if you do a lot of AE work.
All in all though you are not really doing anything to really compromise the quality for HD certainly not for YouTube.
best wishes
Neil
http://www.patience.tv