There is a way where your clips are all converted and then you edit with those clips, and then they are replaced with the original ones for the final rendering output.
Not quite sure HOW it works or how you do it. I've been wanting to know my self for editing 5DMkII footage.
Canon EOS 5DmkII + BG-E6 + Canon EOS 40D + BG-E2N + Canon EOS 33
Canon 17-40 F/4L
USM + Canon 24-70 F/2.8L
USM + Canon 28mm F/1.8 USM + Canon 70-200 F/2.8L
USM IS + Canon 85mm F/1.8 USM
Canon Speedlite 580EX II + Canon Speedlite 540EZ + 2 x Nikon SB-80DX
Cactus V2s Wireless Trigger - 5 x
Cactus V2s Wireless Reciever