Those holes are "alignmernt lugs" used by the machinist that intially sets the block "up" for machining. All the other dimensions "key" on those two holes.
When installing the "lip" (rear), as Bear says, curl it into a cup (we use a spray paint "cap"). Be sure the bevel is "in"
Apply a 1/8" bead of Ultra-Black in the groove, and a contiguous "dab" where the ends of the lip seal will sit. Put the strip in place and set the pan on it (no bolts). Allow to set over night. Trim the rail gaskets to fit. No "overlap" of gaskets. The front may also need a little trim, depending on the brand of gasket. Lay it all out and check before "gluing" anything else "down". Remove all of it except the lip seal (cork strip). Put another bead of RTV around the bolt holes at the rear, and in a single action, over the entire length of the lip seal (again, 1/8" bead is all you need). Put a 1/2 long bead where the timing cover, block and pan all come "together" (across the rail to the timing cover). Add the rails and the front "lip". Put another bead over the strip and around the bolt holes at the rear (SPARINGLY) and another 1/2" bead at the front. Carefully lay the pan in place and start the four REAR bolts. Next, start the front two that go into the block (not timing cover). EASE the rear bolts down "snug" (not tight yet). Front ones next... Install the rest of the rail bolts. Snug tyhe front ones again, and then start the four in the timing cover. Starting in the center of the rails, begin snugging all the bolts, alternating "side side/front back". Allow it to sit over night again. Tighten the bolts. 18 lbs. is "spec", but I've found that to "squeeze" the gasket out if Felpro. So, tighten them until the gasket starts to "move". No further.
This process has proven to work well with the stock type gaskets. Again, as Bear says, a LITTLE. A "lot" is NOT "better". No glue of any kind necessary on any of the "flat" surfaces of the pan, block, or cover.
All this can be eliminated by using the BOP 1-piece pan gasket, similar to those used on modern Ford and Chevy V8s. We've installed several and they are VERY good.
p.s. Howdy Rob... (:-