Designate one folder for your eqlive use, and another for eqemu use. Since I neither know what your existing folder path is, nor what you copy to, I won't try to tell you exactly how your shortcut is to be setup. What follows is merely a guideline.
Your eqlive folder can be patched as often as needed to play on Sony servers. Run "C:\path\to\your\eqlive\folder\everquest.exe" to play eqlive.
Your eqemu folder should never be patched unless the dev team says the server code is now compatible with live. You should run
Code:
"C:\path\to\your\eqemu\folder\eqgame.exe" patchme
to bypass the patcher and start the game.