Just a few notes on connecting the stock heater to an FJ20 engine: -
It matters not which heater pipe is IN or OUT.
Lose the stock 510 heater tap, it has and always will be a piece of crap.
Fit a Bluey type tap, it is all plastic and virtually failsafe/leakproof etc.
The passenger side hose from the heater has to do a complex double 90deg. bend as soon as it enters the engine bay to clear the head of the engine.
I used two 1/2" copper water pipe elbows soldered together to achieve the abrupt change of direction.
Pics. available
By cables, I assume you are referring to the heater/vent cables?
Well, the "heater" cable routes to the heater tap wherever you have located it.
The "vent" cable connects to the demister/cabin flap arrangement to direct the air into the cabin or up to the windshield.