You'll either need an EPROM programmer or (more likely) buy a new ROM from someone who has an EPROM programmer.
You remove the old ROM (which is a separate chip next to the CPU).
http://amiga.resource.cx/photos/apollo4060,1
Then you plug in the new ROM.
MACH chips do not contain executable code, they are CPLD's (programmable hardware chips) which hold the hardware design (logic gates) of the board. They are the guts of the accelerator and what makes everything work.