Ideally, a manifold, the gasket and the head line up anf you get a perfect continuous chamber.....
But how do you know how the runners in the manifold line up with the heads when bolted together?
Start by setting the same gaskets used to port the intake onto the heads. The gaskets match the intake already. If they don't match the head, get to work.
I think if the intake runner is smaller as opposed to bigger is better.
You have to have a lot of work on the heads in order for any intake mods to make any difference.