Hi David
I have not used premiere pro and therefore can't really comment on the premiere pro workflow. However, any editing system is going to struggle with h.264 files as they are in a delivery format not an editing format.
So my advice would be to convert them into an appropriate editing format that suits your workflow. In addition, I would adopt a strategy to back up your source material. This, apart from giving you piece of mind in the event of a data loss, gives you options later to transcode to a different codec if needed.
Declan Smith
http://www.madpanic.tv
FCS3 / After Effects CS4 / Combustion / Canon 7D / Canon XL2