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Patching is simple if you use VisualBoyAdvance as your primary emulator. All you need to do is use your file manager (Windows Explorer or the Macintosh Finder, for instance). ROMs patched using this method are not touched at all; simply trash the patch and the ROM will be played as-normal.
Place the ROM you want to patch in the same folder as the patch.
Rename the ROM file so that it matches the name of the patch. (You may not have to add .gbc to the name.)
Open the .gbc file in VisualBoyAdvance (or, if you've set it to open in VisualBoyAdvance, double-click it).
This process is also an easy method which works on every emulator, but it's also non-reversible; changes made to the ROM are permanent, so it's best that you make a copy of your ROM. You will need to download an IPS patcher - if you're running Windows, use Lunar IPS (http://www.zophar.net/utilities/download/lips100.zip). If you use Mac OS X, try using UIPS (http://www.zophar.net/utilities/download/UIPS.sit). Note that the order shown here may vary with other IPS patchers.
Load the patch application up.
Click the "Apply Patch" (or similar) button.
Select the IPS you wish to use and click Open.
Select the ROM you wish to apply the patch to.
Load the ROM up. It should then work and changes are permanently applyed to the ROM. You may delete the IPS file as it will no longer be needed.