I find more complete instructions to be included in the below, which also provides information on what to do if the patch doesn't apply to begin with.
http://www.rockbox.org/twiki/bin/vie...ideToCompiling
I typically start with putting patch files in the master Rockbox folder containing the Rockbox software folders (that is, in the master Rockbox folder containing the apps, firmware, tools, etc. folders), and then applying the patches from that folder as well. If that doesn't work, I have had success in putting the patches in the folders that they will apply to (e.g. a patch to apply to the jpeg.c file in the apps/plugins folder, where jpeg.c is found) and then applying the patch from that folder as well.