Put the ROM files in this folder:

    48.rom        the 48K ROM
    128-0.rom     the 128K ROM, bank 0
    128-1.rom     the 128K ROM, bank 1
    trdos.rom     TR-DOS, needed for .trd and .scl disks

Then start the tool and set  Settings > Misc > ROM  to "Custom ROMs from
ROMS". Until you do that the tool uses its own built-in ROM and never
reads this folder.

See README.txt, section 2.
