I don't do this with all, but if I have a problem child....
3M the gasket exactly where you want it, and don't be afraid to do it around each port, put some on the head, some on the gasket, then attach glue to glue after the glue is tacky.
Do whatever you are going to do on the china walls, Right Stuff, Motorcraft, end seals, your choice
Just before you set the intake on, put a swipe of RTV around each port on the now locked solid intake gasket, and bolt the intake on. The wet RTV will initially let the intake move as you tighten and leaves your gasket staying in place (the ends anyway, the middle is held by the head gasket tabs), but I like to think it helps seal things up afterwards on the problem children too.
Remember though, sometimes on odd combinations the intake bolts can hit the intake before the intake settles down completely. So you may want to do one gentle dry fit and look into the intake bolt holes to see how the threads line up.
If the threads are above the centerline of the intake bolt hole, you are in trouble because the bolts will hit the intake as the threads try to pull it downward. At that point you either open up the intake holes or dig deeper to get things fit properly, basically fitting the manifold to whatever someone else did to your block