I put a bead of RTV around the coolant port and two dabs in the middle flat area. Then lay the gasket in place and set the lower intake on. I put a few bolts in the intake to the block lightly (just to put some light even pressure on the gasket). Let it sit for a few hours or overnight. Remove the lower intake and make sure the gasket is still fitting correctly, if not repeat. Setup your front and rear with the RTV or rubber gasket (or combo of the two) and let setup. Then put a light coat around the other side of the gasket were the coolant ports are. Install the lower intake.
putting the intake gasket on this way helps make sure its not being distorted, lines up, and does not get moved around. The RTV glues the gasket to the heads and since your not putting a torq load on it or heat cycling it you can move it around if when you pull the intake the gasket has moved. Then when you go to install the lower for good you wont have to worry about the gasket fitment when your in the ever so great awkward position of installing the lower intake.
I have always used the 1250 "print-o-seal" fel-pro gasket and still use if anything a light coat of RTV on the "seal" part and a light bead on the non-"seal" side. I am sure with your big ol' ports a different gasket is being used