You want to wire your volume controls up like a Jazz bass or Rickenbacker.
So instead of the pickup wire going to the outside lug on the pot, they go to the middle, and the output comes from the outside lug. The tone controls also get wired to the middle lug where the pickup wire is connected.
Keep in mind that when both pickup are al the way up, one tone control will effect both pickups. Also when you turn a pickup partway down, you loose some high end because of the loading of the pot.
You can follow this Rickenbacker schematic for a 2 pickup, 2 vol-2 tone guitar.