Three main points:
1. Once the manifold is off, use the screws to pop the nuts out of place on the old manifold so you can put them in the new manifold.
2. When putting the manifold back on, do not tighten one side all the way before starting to tighten the other side. Think of it like putting on a tire on a car. Get one side slightly fastened and then do the same on the other side. After both sides are more ore less attached then tighten both sides. This will make sure there is not tension pulling in one direction causing one side to close up.
3. Do not tighten so hard that the manifold starts to bend. My rule of thumb is to tighten to the point where you can just start to see the screw showing through the top of the nut.