hey there Nate
it’s best not to edit the Native H.264 files.
unless you have prem CS5 and the DSLR sequence presets.
It’s best to use mpeg streamclip from https://www.squared5.com (it’s free)
to convert your clips for editing.
to save some time you can just make exact name and extension copies of all your clips
then in prem, select all the native 550D clips, right click and make offline.
then reselect and link media, navigate to the new Proress or XDcam EX clips (converted through mpeg streamclip) and re-render the timeline.
maybe change your timeline sequence settings or simply copy paste all the clips to a correct sequence.
once you done render out as quicktime animation codec (highest possible quality)
then encode that rendered clip with Quicktime pro back into H.264
i know it seems like a bit of a long process but that is how to get the best quality out of your clips for H.264 web uploads.
Vimeo has some nice tips on quicktime encoding settings.
just play around with the bitrates to get higher quality or lower file size.
hope that helps?
Greg
https://gregbrand.co.uk