I'm putting 80% quarters on my car. The car currently does not have an engine.

Do I need to put the engine in to line up the quarters before I weld them in?

Nope, all you should have to do is make sure the car is relatively level and supported by the areas where the car will naturally be loaded when on the ground. This insures that you won't get any unforeseen bulges or additional stress in a panel once you set the car back on the ground.

Great, thanks!

For an 80% quarter i would be using panel adhesive rather than welding it, no heat to warp your panels and no place for corosion to start, just my opinion.....

Im going to weld mine on that im currently doing however for anybody who wants to glue panels on, this seems to be a good introduction to it.

http://videos.streetfire.net/video/1965-Chevelle-Quarter_174149.htm

Pay close attention to the measurement of right side bumper bracket to left side bracket. In my case, it wasn't noticed and the car is wider than it should be.