I use whatever silver stuff Napa sells with a brush in the can, but the copper stuff works well too
Chase every hole, it doesn't need to be a bottoming tap, a cheap thread chaser works great too.
You only need 2 opposing bolts per tube, but more can't hurt. The key is tighten them all evenly like you would any other flange. Sometimes guys are careful in a build, the get to the headers and over-tighten the easy ones. Sometimes it takes a bunch of different wrenches, 1/4 inch drive sockets, 3/8 sockets etc to be able to tighten them all the same, but in the end if you do, they'll last for years and years with no leaks.
The manifolds are a bit easier, one piece machined flange, so they can be zonked down with a little less thought, but be careful and you'll be happy with the results