It is completely trivial; you can do it with Lunar IPS
or any number of other programs. Just direct the program to your modified ROM and a copy of the unmodified ROM, and it will make a patch. I'm not sure what you're expecting?
Just make sure that your unmodified ROM is a recognizable dump that is readily available on the Internet. You'll also want to calculate the hashes for the unmodified ROM using http://www.romhacking.net/hash/
or something similar. (That way other people can make sure that they're using the unmodified ROM for which your patch is intended.)
If your patch ends up being approximately the same size as the original ROM, then you've done something wrong – but the only thing you can really do wrong is selecting the wrong unmodified ROM.