I hate that permatex #2 brown crap. I can't think of an application any more where it would be useful.
Use Ultra Black or Ultra grey, put a bead across the front and back of the block, then put a VERY light coat on the manifold and head around the water passages. I generally throw a glop or 3 somewhere on the head (away from the ports) to stick the gaskets too just because I've already got the tube in my hand and it helps keep the gaskets in place during assembly. Drop the manifold straight on, start all the bolts, then tighten evenly starting at the middle and working your way side to side and towards the ends of the block. Wipe the excess RTV off the ends if you feel like it.