The exhaust manifold is threaded where the two bolts go into it. The third bolt, fender side, is a nut and bolt. Look closely when you have the two separated for wear. The gaskets tend to wear on the manifolds creating grooves that are hard to seal. I have had a set that needed two gaskets to seal up. When assembling back to the engine, snug the three bolts first that hold them together, then tighten the bolts to the head. Always hold the weight of the manifold till you have enough bolts in the head to support the weight. I like to tighten the bolts highest up on the head first then the lowest ones, that way the bolts are not lifting all the weight of the manifolds. Once you have all bolts snug, tighten the three holding them together, then starting in the center of the head, work your way towards each end.
The two small locating studs on each end are also threaded in to the head, you can add bolts if you are have sealing issues out on the end, just don't over tighten them.
If you have the time and money, you can get the manifolds surface. With the three center bolts tight, have both manifolds machined as one unit, this will insure a flat surface and positive sealing to the head.