Your best bet is to make a copy of your EQ directory for EQEmu use and make the changes there. At the moment, the emu is compatible with live, so you can switch between the two just by changing your eqhost.txt file to point to either Sony or EQemu, but there is bound to be a Sony patch soon that means you won't be able to play the EQemu version, unless you maintain two directories.
//Derision
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