well i downloaded the patcher used in the tutorial, i think it was Tsukuyomi UPS, i just google it..
then i selected "apply patch to a new file", you can see there three input box..
1. UPS Patch to apply - (select here the UPS file)
2. source input file to apply patch to - (choose here a clean emerald rom)
3. target to write patch file to - (choose here a clean emerald rom different from the rom you used in no. 2
i don't really know why you must need two roms but that is the only way i made it work for me, might as well try for yourself hope it helps..