The engine being in or out won't matter, what matters is that you have to get the car up on jackstands and perfectly level before you start adding subrails or the rollbar. Once those are welded in the car will retain that shape forever, so you want it to be as plumb as humanly possible. Get the tires up off the ground totally.

They really do make a difference too. After we did my Son's Capri drag car you could jack up one corner and the entire side would lift up. Before that it was like a wet noodle.

Don