Originally, I had a mental image of a big vise, mounted into a contoured inset in the front of the bench. It sounded neat, and clean. In the end, I didn't like the way it turned out, but I'll explain the layout for the benefit of anyone who wants to try.
Laying out the contour of the vise took a little head-scratching, but I eventually figured it out. I inserted a piece of plywood into the face vise that was already on the bench. I clamped the Emmert (upside down) to that, and was able to trace out the profile of the rear jaw. I also traced the rear vise onto two separate pieces of plywood, to make patterns for routing. The first pattern had a cutout for the mounting plate. The second one was just to rout out the jaw profile, all the way through the bench. 
To cut the jaw profile, I used a top-bearing pattern bit (bearing between the shank and cutters) to follow the pattern, and cut the profile as deeply into the bench top as possible. But the top was 3" thick, so to finish the cut, I had to flip the top over, and finish the cut with a bottom-bearing (bearing at the end of the cutter) bit, that would reference against the surface of the first cut, and bring the shape all the way through. The second template was used to cut the recess for the mounting plate, aligned with the first cut.The most important thing I can say at this point in the mounting procedure is NOT to drill the holes for the mounting plate. This is critical. Don't do it.
For the purposes of fitting the rear jaw to the bench, it's very helpful to remove the front jaw and the beam, to cut down on the amount of weight that's going to be mounted and removed, since you'll have to do that a few times. Because the mounting plate has a sort of L-profile to it, you'll need to trim away some material to clear that part of the vise. You're also going to need to remove a large amount of material to clear the barrel that allows the vise to rotate. And, depending on the thickness of your bench, you may need to hog out a trench to clear the beam, as well.Bear in mind that you will ultimately need to be able to clear the beam when the vise is rotated to 45 degrees, not 90, as this will be the closest that the edges of the beam get to the bench top. Also bear in mind that, at this point in the sequence, the front jaw is probably disconnected, so it is probably worth coming back to adjust the trench later.
There are two holes in the mounting plate, behind the rear jaw, that will enter the bench horizontally. These screws are strong enough to hold the rear jaw in position while you trim and shim the space you have to cut out to get the face of the jaw to be parallel to the front of the bench.
Original instructions for the vise say to mount it about 1/8" forward of the front edge of the bench. I can say from experience that 1/4" is better. The reasoning is that it's easy to bang your work against the top edge of the bench while you're rotating the jaws, and that clearance will help give you enough clearance to help prevent that. I know the prevailing theory is that you should be able to clamp long pieces that stick out past your vise to the front edge of the bench. There are simple solutions to the 1/4" offset, I promise you. And they're easier than fixing something that gets damaged while you're trying to manipulate it in the vise.
All the above said, offsetting the vise does make it harder to make sure that it's actually in line with the rest of the bench. My solution was to use a simple 4' piece of extruded aluminum T-track as an improvised straight edge. Held up against the rear jaw, a long straight edge will either look parallel to the front edge of the bench, or not. I aim to be within a few 64ths over that 4 feet. I'm sure others will be more finicky than I was. That vise is heavy, and I got tired of mounting and removing, mounting, and removing.
When the vise is aligned to your satisfaction with the front edge of your bench, this is the time to lay out and drill the holes for the three screws that go through the top of the mounting plate. Take your time, center punch or transfer punch the holes. These will permanently fix the alignment with the front of the bench.
I was really excited about the vise, but the install looked like crap, and I had other jobs lining up. So, I made the decision to cut a square notch out of the bench. I put the bench top on a cart that was at the same height as my bandsaw to make the rip cut down the length of the bench. I used a track saw to make the crosscut that completed the notch.
When everything was put back together, the vise was about an inch and a half away from the front edge of the bench, as shown. This doesn't bother me. It's a little more clearance than I need, but the vise itself is 16" wide. That offers enough support to the work that a missing inch and a half will go entirely un-noticed. Since I put up my original blog entries, I've read about other bloggers stick with the inset method, carefully carved. I admire their tenacity, and I'm sure their end results are more than satisfactory. This is simply how I chose to mount the thing. If I were to build a new bench with this style of vise in mind, I would most likely laminate most of the top, leaving the last 2" or so until after I'd actually mounted the vise. I would simply edge-mount the vise, and then build out the bench top to be flush with or slightly behind the rear jaw, because it's easier to mill that last piece down to the thickness you want, than it is to trim and shim the vise to get the offset you need.
