Using Tekken 4 as example. I have the following files
roms\NM00004 Tekken 4 JAP\NM00004 TEF3, Ver.D a025671124888a.ps2 (I got it from the pinned post link for the actual dongles, clicked NM00004 Tekken 4, downloaded NM00004 TEF3, Ver.D a025671124888a.bin.gz, extracted the file NM00004 TEF3, Ver.D a025671124888a.bin, renamed it to NM00004 TEF3, Ver.D a025671124888a.ps2. Yes you must rename it. If you don't it will not just work.)
roms\NM00004 Tekken 4 JAP\boot.elf (I got it from the pinned post link DONGLE_FILES.7z, went inside TEF3, Ver.D since the folder matched the names above and copied just the boot.elf file, none of the other files)
roms\NM00004 Tekken 4 JAP\tef1dvd0.chd (to get it I googled for: mdk.cab tekken 4 chd)
And the following tekken4.acgame to launch the game
[game]
name=Tekken 4 JAP
gameid=NM00004
[data]
subdir=roms/NM00004 Tekken 4 JAP
elf=boot.elf
dongle=NM00004 TEF3, Ver.D a025671124888a.ps2
card=
mediasrc=tef1dvd0.chd
media=DVD