My guess would be that you just haven't found the by-pass valves yet. You may have to remove one of the drawers in the cabinets to access them.
It may only have the discharge valve on the water heater, so you would be filling it up, but not getting anything through it.
Also, keep in mind that when you finally get things working, you don't want to "vent" the water heater. If there is air in the top of the tank, it will act as a cushion for your pump and system....so don't blow out the relief valve.
You may have to trace out the water lines....pulling cabinet drawers out, etc. It's probably a good idea anyway....you'll learn a lot, and find stuff you didn't know you had!
Good Luck:)