Are you going to reuse the headers? If so leave them in place. Might have to unbolt them at the collectors. Tie off the headers to the side and drop the new motor in. Much easier than fighting with fitting the headers in afterwards.
You might get away with leaving one on and turning the engine a little to jockey it out. I think I can remember one install where I had the passenger side on and then when I got the engine a few inches from sitting down in the mounts, I then installed the driver side. That could have been on a Camaro though... And it depends on the brand of headers you have. My Doug's are long branch and there's no way you could come close to installing either one until the engine is all the way down.