Depends who does the fix, some fixes are the complete updates. Some fixes as you say are just the EBOOT.BIN and any other files that need to be re-encrypted, and the standard pkg required files like param.sfo etc. The instructions are normally very clear as to if it is a full update or just the fix. If it is just a fix you install the official updates first and then any fix.
Just be aware that the game code (sorry forgot the official name for it e.g. BLES00001) needs to match the version of the game you have. Otherwise the fix will install in a completely different directory and make no difference to your game. :-)

