Hello Ryan Arndorferm,
Are you still experiencing problems? There are some scripts on the manufacturing tool with the parameters to load different boot sources and some versions of the manufacturing tool also have a qsp-nor .vbs file for some boards (the i.MX6UL EVK should be included). Alternatively, the new UUU (Universal Update Utility) is a bit more flexible so you may also want to look at it.
Regards,