Yep, OS X is a *nix system, and probably will have patch. You can simple test it by typing 'patch -v' (display version number) in the command console.
When you make a patch (using a diff program), the new and old file are compared. Only the changes are saved to a patch file. So, a patch file will contain information about which lines of code to change. The program is clever enough to detect certain code changes. E.g., in the original patch file it say line 27 has to be changed from 'echo "test";' to 'echo "This is a test message";' However, since you have also modded the file yourself (added code above line 27) this line is now another line number. But patch will still be able to find the correct line and change it.
If you know a bit about programming and script, take a look at the patch file. Line with a - will be deleted, lines with a + will be added to your scripts.
Instructions to patch PunBB can be found here. The patch file from 1.2.5 to 1.2.6 is here. The patch for other version can be found the the download section.
I suggest you make a backup copy of your script, run patch on that and see what the result is.