That's just it, what holes, for what?
If your talking about a drain, I would go with 1 1/2". That means if you want to use 1 1/2" pipe, the hole will be much bigger. You need to look at bulkheads for 1 1/2" before drilling your tank.
Now if you want to drill your tank for a closed loop, you need one suction hole, and two or more return holes. The amount of holes and the size of these holes depends on what pump you are going to use, then size accordingly. Just remember, get your bulkheads first so you know what size holes to drill.