Everything I've read indicates that the factory aux tank uses an external transfer pump, and that it doesn't pump directly to the engine. The parts diagram certainly appears to show the aux pump going into the main tank, and a separate line leaving the main tank toward the engine.
It's...
What kind of dual tank setup do you have?
The factory dual tank, I believe, just refills the main tank from the aux tank, so I don't think that would affect anything you're doing.