I have done exactly this - PWM controlling an AEM meth pump.
As suggested, I used the "alt boost". It works great. PWM frequency of 30hz and I think I used a spare ignition output (as already said just assign something with a high current transistor).
Then what I do is I connect the wires from the low level switch on the methanol tank in parallel with the vems warning output.
The meth switch or the warning output form vems triggers a relay that illuminates a check engine light and cuts power to the boost control solenoid.
This scheme, especially using the "lean detect" with a properly deifned lamda target table crates a pretty good failsafe. No methanol or a lean conditions cuts power to the boost controls solenoid and boost returns to base the wastegate setting.
Makes it pretty much idiot proof.