The sources are widely available. You can a have a look at them and see how it works.
The PIC firmware configures the FPGA with MINIMIG1.BIN file. No matter what it contains.
The Minimig FPGA file contains a ROM with bootloader for the external 68000 CPU. This bootloader uses Amiga floppy DMA controller to talk to the PIC. The PIC sends an Amiga ROM file which is received by disk DMA and put in the RAM buffer. Then the 68K CPU copies it to the specified location.
In the latest firmware only two ROM sizes are supported: 256KB (no need for mirroring to 512KB) and 512KB.