I bet you're going to get as many opinions on this as there are guys to have them.

I have known of folks doing all sorts of things with RTV, and some with great success. A few I can recall would toss the rubber seal and just lay a big fat bead of RTV on the block, let it cure off a bit, and install the manifold. Personally, I preferred to keep the rubber seals, and use a neat small bead, no bigger than an eighth of an inch, of flexible sealer on the block, set the rubber seal in place, lay down another bead of sealer and very carefully install the manifold so as to not knock anything off kilter; after everything was all torqued down and set, I'd clean up the squeeze-out. It usually worked fine, and my success rate was probably as good as the guys who used the RTV build-your-own-gasket procedure.