Your Doug's headers should have come with some installation instructions ---- I know mine did. Since you're doing an engine swap anyway, the easiest way to do it is to set the headers in place while the engine is out. If that's not an option, then as I recall the installation procedure is to do one side at a time. Support the engine with a floor jack, remove the long motor mount bolt on the passenger side, use the jack to lift that side of the engine to get some room to work, then drop the header in from the top. Lower, re-install the bolt (!), and repeat the process on the drivers side. Getting the flange bolts started and in is tough and you will expand your vocabulary doing it. Be patient and persevere. I'd recommend replacing at least one flange bolt on each end of the head with a stud and nut so you'll have something to "hang" the header on while you're futzing with the rest of the bolts. It might be easier still to use studs for all the fasteners - that way you could slide the header out on the studs with just a few threads showing, providing more room to slip each nut on and get it started.
Other tips. That brake line distribution block you probably have on the inside of the drivers side frame rail --- plan on biting the bullet and relocating it to the top of the frame rail, otherwise you're likely to have clearance problems there and the heat is going to tend to cook your brake fluid. I highly recommend replacing the starter with one of the newer "mini starters" (I really like this one: RobbMc Performance Products - Pontiac Starter
It's a quality piece, the solenoid can be 'clocked' to any position you like to get it away from the heat, and the company is great on service and support), otherwise you're likely to find that in order to R&R the factory starter you'll have to loosen the drivers side header. Lastly, pay attention to the lower control arm bolts. If the "nut end" is towards the header you may have clearance issues there - I did. I wound up turning the bolts end for end so that the bolt head is next to the header tube (and it's still pretty tight there). Of course this also means if I ever have to R&R the lower control arms... yeah, the headers are going to have to be moved out of the way first. I see you have a 66 -- if it was a later model with the 'back drive' interlock between the steering column and the transmission, you'd have to either completely discard that and run without it, or spend some time re-bending / re-engineering the linkage to make it fit around the header and still work.
Make sure you use high quality gaskets (I like these: Remflex - Pontiac V8
) and don't forget the anti-seize on the fasteners. Yeah, you may have to check and re-tighten them periodically but that sure beats having to deal with a seized one down the road.