That is a good idea to toss out the end rubber gaskets and it is a good idea to use silicone around the water ports. You need to look at your head and intake to see how rough they are. Sometimes electrolis eats small amounts of the metal away. I would not put silicone around intake ports unless you keep it a distant away from the port. You do not want it to suck the silicone into a valve later on. I would just put a little around the water ports (and this should help hold gasket in place) and maybe thicker if it is rough- you need to fill in all voids. And like the Dawg said a good bead in the ends where the rubber gaskets were is good too- lets intake fall into place.
http://www.edelbrock.com/automotive_new/misc/tech_center/install/2000/2101.pdf
you can copy and paste to read the instructions for you manifold