Tony,
Sorry for the delayed response. The middle handle is for carrying with one hand (while carrying something else in the other hand). If I am feeling lazy I can use the outer handles with both hands and just carry the sub by itself. So I guess you could say that the three handles are for balance.

I too was worried about drilling into the sub, particularly for the handles. The 'timber' is only about 15mm thick (9/16"?) so I added another layer of plywood to the top of the box before carpeting. This plywood is glued and screwed. The screws for the plywood, handles and corners are all chosen so that they don't protrude into the sub. It still works so I guess I didn't hit anything.

Mark