Just a quick update, I was able to get in contact with the creator of the MicroNova Mercury board. He was VERY pleasant and accommodating, and answered my questions about programming the Spartan FPGA. He told me that Xilinx/Digilent are very protective of their source code and hardware, so I won't be able to program
this thing (or the Mercury board) using the Adept software like I'd hoped. That being said, MicroNova wrote their own utility to program the FPGA using the circuitry provided in their schematic. The utility can be downloaded from this page:
https://www.micro-nova.com/mercury-programmer
From what I understand this is effectively a replacement for Adept that allows me to load my bit file and will program it straight to the flash on the Mercury board. We'll see how that goes!