Spotting the correct BIOS
as you probably guessed, SYSTEM246/SYSTEM256 do not use the same bios than retail PlayStation2's
you will need an arcade bios, otherwise games will NOT work due to a plethora of API differences on BIOS modules like FILEIO, MCMAN, SIO2MAN and more
fortunately for you, the program automatically identifies the appropiate bios, and it may even identify which system2x6 variant it comes from
here you have an example

you probably noticed it, but just to be sure:
arcade bios will be identified with the word COH-H, which is the model number prefix for arcade PlayStation2 units
for SYSTEM246, you may pick whatever system246 bios or system256 bios you want. however, for system256 games we recommend you stick to the 256 bios