I use the complete gasket kit. We just put an intake on my son's 360 last night.
With the intake on and no gaskets, the bolt holes lined up. With all gaskets in place, the bolt holes are a little higher than the holes because the gaskets (especially the end ones) are not compressed.
What I did was try to put the intake on as centered as I can get it. The blot holes will be just to the bottom of the intake manifold holes. Start a bolt on each of the 4 end corners of the intake biasing the bolt towards the bottom of the hole and try to get the threads just started a few turns each. Try to get all 4 corners started, then work your way to the center. I had to run down the second bolts from the "corners" (no torquing yet) to get the center bolts installed on each side of the carb. That brought the bolt holes in better alignment. You have to try to catch the threads toward the bottom of the bolt holes. But always try to get as many bolts hand started before tightening if possible.