The holes should be the right size for the bulkheads you intend to run in those holes..
Also.. If you are drilling do yourself a favor and run a bean animal drain system.. It requires 3 holes but is superior to a herbie system.
http://www.beananimal.com/projects/silent-and-fail-safe-aquarium-overflow-system.aspx
3 x holes for 1" bulkheads are perfect for a 110g tank..
As to if you drill holes for the returns thats your choice.. You can or just do over the top returns..
Don't forget anti-siphon functionality to prevent the returns from draining too much water in a power failure situation..
Also.. you really want to know what pump you are using to ensure its suitable..
Surely there is a product sticker on it.. Or post a picture of it with something next to it for size reference (coke can, ruler, etc...)