The end vise will have both jaws made out of 1-1/2" thick oak. The front vise has its moving jaw made of 1-1/2" oak, but uses the edge of the bench as its stationary jaw. So while for the end vise, if we mount it lower, we can make both the jaws deeper to compensate, for the front vise we cannot, so we want it mounted as close to the edge of the bench as possible.
So drill the benchdog holes through the MDF layer. Begin by laying out their positions. You'll want these to be precise, so that the distances between the holes are consistent. The vises you are using will constrain your benchdog spacing. My front vise worked most naturally with two rows of holes four inches apart, my end vise with two pairs of rows, with four inches between the rows and eight inches between the pairs. Because of this, I decided on a 4" by 4" pattern.
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Workbenches have flat tops, though sometimes at the rear there is a cavity called a tool well that contains tools and components (and prevents them from falling off). One advantage of having the well set into the top of the bench is that, even with a variety of objects in the well, a large sheet of material can still be laid flat over the entire surface of the bench; the contents of the tool well offer no interference.
I drilled from the mark. That way I could ensure that the hole was where it was supposed to be, on the side where the position was critical. I have two 3/8" bits -- a brad point bit that came with my doweling set, and a perfectly ordinary 3/8" twist bit. Brad-point bits are far more precise than twist bits -- they're more likely to start where you want them to, and they're more likely to stay straight. My problem is that my brad-point bit wasn't long enough to go through 3-1/2" of wood. So I started each hole with the brad-point bit, then finished it off with the twist bit. I clamped a piece of ply on the back, to reduce tear-out.
Synopsis: No room in the garage? Basement not an option? Consider what Ken St. Onge did when he needed shop space: He bought a prefabricated shed and converted it into his full-time woodshop. Because a pre-built shed doesn’t need a cement foundation and is built in a factory, it’s much less expensive than building an addition or stand-alone shop on your property. It can have taller ceilings than a garage and bigger doors than a basement, both big pluses for a woodworker. You can put a shed just about anywhere, too. Here’s a soup to nuts look at Ken’s experience, so you can gauge whether a shop in a shed is right for you.