Are you buying a rack or making one? I would drill the holes in the sides and then find a rack or build one where they would fit snugly enough so there'd be no need for a cover. Thats just how i would do it personally bc im kinda lazy and having to slide out each tub and take off the cover seems like a pain lol but its totally up to you! As far as how many holes i would start out with fewer then see how the temps/humidity are and if u need to adjust it you can always add more holes.