I drilled both of the holes for the snaps near the windshield center strut from below.
Just measure where you want them to be (both of mine are about 2" from the center strut rod and just on either side) and then re-measure from below, put a dot on the underside of the cowl with a Sharpie and then slowly drill the hole - I had plenty of room under there to get at it. Safety glasses and/or a vacuum hose near the bit is a good idea. Once the holes are in, I installed the snap ends using a 90 degree offset screwdriver - one of those you always get with a pre-sorted tool set but never know what to do with.
IIRC, I also have another snap on the edge of the cowl, an inch or so forward of the top of the door. None down the length of the door, and the next one to the rear is the first of the top snaps on the side of the cockpit.
I've never driven with the tonneau on more than the back quarter. Never thought I needed it nor did I want to damage the paint on top of the doors. Like Alan, I also have a clear 3M film along the tops of the doors, but mostly to avoid abrasion from the side window gaskets, when in.