At least for the sandwich cases I’ve built, the bolts go in from the top. Sometimes they’re countersunk, sometimes not - I had worried that bolt heads would be obtrusive, but other than being a little ugly visually, they don’t get in the way of using the board.
Nuts on the bottom are the simplest approach, and then you can just use adhesive rubber bumpons to keep the nuts from scratching up your desk. There are cleaner approaches - see this build I recently finished, which used hex nuts held in place from the bottom by screws. Even then, you’ll probably still want bumpons for added protection, as well as give the board some tilt; fat bumpons on the back edge, small ones on the front.