I'm glad too see you went with 2 tanks. The others brought up nice points about taking the stand apart.
Depending on how much flow you want to run through your refug, you could just run the drain into the fug and not split it. You will plumb it like the last drawing short of the split drain. You'll drain into the refug, then it will go into your skimmer section and so on. Just a little more easy IMO.
The drill bits are cheap as 2Quils mentioned. They are a diamond tipped hole saw. I paid 13 bucks for my 1 3/8" bit through Glass Holes.
Edit; Oh yea, you wont find the bit at the depot.