You have to figure out how the second pump is wired.
My second pump is wired using auxiliary output 2 (pin B2) which uses boost and tps to turn on the ouput. It works fine with the engine off. My main pump is wired to the fuel pump output and it will only come on for a prime and then it has to see rpm.
Your second pump could be on pin B1 (aux. 1) and would need rpm and tps to come on. Aux 3 and 4 use coolant temp or air temp and tps, mph and tps. It is unlikely yours is wired using 3 or 4. Or, you could be using a racetreonix harness with something triggering the pump other than the xfi.