Using VHDL with the Mojo V3 FPGA
Use Xilinx ISE to build a design for the part, then use Mojo Loader to load the bitstream into the board's flash memory. (Due to some unfortunate design decisions on the part of Embedded Micro / Alchitry, there is no way to load a design directly onto the FPGA using the Mojo's USB interface.)

If you aren't familiar with using Xilinx ISE, here is a brief tutorial on using it with this board.