But for anyone in the future wanting to know, it does need to be set up manually. I think the newest AEM z32 start up calibration file has it already set, but mine didn't. LS8 and Injector 11 on the output configuration need to be set to VTEC and pin enabled. Just set to turn off at (active column set to "less than") 5300RPM(This can vary depending on tune and mods).
After that, I had no problem bringing up boost off the transbrake and 2 step due to much needed torque to get the convertor going.