What exactly did you hacked? It’s strange because, if you’re actually able to hack roms, you should already know why doing what you did would not work.
I dont really know if you understand the proccess, so let me explain it all: xcopy’s functionallity is to apply/remove the encryption from the instructions present on the roms. Not all rom files contain instructions, some of them only contain data, so applying xcopy on these would make no sense. Anyway, lets say you want to hack some of the assembly code contained in a CPS2/3 rom: to do it, you first have to apply xcopy on the right file, to remove the encryption. After that, you hex edit the file (to this part you have to be actually good on reading assembly, so its not up to me to tell you how to do that) making sure to not alter the number of bytes on that rom file (obviously). After you hacked the right bytes, you have to encrypt it back so the emulator can read it properly, so you have to use xcopy again, now in encryption mode. After that, you can pack the modified file with the other files to form the complete rom, zip it back and it will be read to be used on emulators.
As for the offset, it depends on which file from the rom you hacked. If you press the " " icon, it will say exactly which offset to use, depending on which file you hacked.