if you are only replacing the seals the heads and manifold should still be lined up good. dont loosen the heads if the manifold fits correctly. if it doesnt fit (gaps around the flanges or wont go in), then the heads need to be shifted and tightened back down while checking the manifold fit(install new head gaskets)...but dont install it with the heads loose, it wouldn't seal like that.
lube up the orings with motor oil and roll them up on the manifold flange or head flange till they will stay there, line up the manifold in between the heads and roll them off the flanges into the gap. it should hang by itself then. if you have the s&s bracket that comes up from the center case bolt...stick a 3/8 bolt thru it with a nut on it, to help hold the manifold still. if you havent put that on yet, might take a minute to get it bolted on, adjusted and lined up before you even try.
open up the clamps, stick one on and snug it up a teeny bit...stick the other one on. gradually tighten them both up, feeling around the inside to make sure the mating surfaces stay lined up. tighten them up till its metal to metal.(the clamp to the flanges). they will get snug all of a sudden once the orings are smashed in.
its just a pain. might be easier with somebody on the other side of the bike holding the manifold still/inward if you dont use that particular carb support bracket. tedious.