The holes you choose does not matter as long as the boot sits in the middle of the board (equal overhang).
+1 you're looking for equal overhang. There's no such thing as no overhang (unless you're riding like a 12" wide board with size 6 boots!). When I set up bindings I toss the boots in them and ratchet them lightly down, then rock them back and forth while pressing the edge into whatever surface I'm working on. Should be able to get about 60 degrees or so of lean angle in each direction.
If you got a wide board and more angle than that, just make sure they're centred...