You mean align the glass and wafer, right? Not the lithographic steps with a mask.
I would put a drop of the adhesive where it will go, align with a microcontroller and then place in the oven but maybe I'm not understanding your process or dimensions...
Have you fully Cured the SU-8 on both wafers. You can cure the SU-8 on the silicon wafer and partially cure the SU-8 on the glass wafer. Place wafers in contact and then put in UV Cure Oven. Both wafers must be flat or there will be gaps.