This guide should help you in your goal of patching your ROM. This guide is applicable to most ROMs and patches but makes some assumptions about the patches and ROMs used:
To remove a ROM header, it’s probably easiest for you to remove the header using NSRT, as well as verifying it is the correct region, version or any other specifics about the ROM. First make sure the sure in the NSRT Preferences → Headers section Remove Headers is selected, click Apply and OK. Rescan the ROM you wish to patch and it should now be header free.
The patches come in various formats, UPS, IPS, BPS and BDF which is short for BSDIFF. There are numerous ways to apply patches, and I will touch on just a few of them.
For OS X I highly recommend MultiPatch.
Use this PERL script IPS.pl.
ips.pl rom.sfc patch.ips
For BDF / BSDIFF patches you can install bsdiff form source through Homebrew on OS X and should be avaliale already on Linux, then you can run the command:
bspatch old_file.sfc new_file.sfc patch.bdf