the eqclient.ini file is likely the file your talking about.
you can run with multiple installs of EQ, or as mentioned above Denethors guide works and is kinda neat (makes computer think it has multiple installs).
there are 2 programs i know of that will handle different eqclient ini files from one eq install, and they both come from lavishsoft. isboxer (as mentioned above)works great. and there is also WinEQ2.
im currently running with WinEQ2 so that i can use multiple eqclient ini files (high graphics on my main toon, far clip plane / particle effects for my puller, and bare minimal settings for any other toon).
Isboxer and WinEQ2 also both allow you to set custom keys for switching to a specific instance of EQ (as does the MQ profile system). Isboxer also allows key broadcasting (which is rather nice for some things).
edit, forgot to mention, ive been using Isboxer or WinEQ2 and other eq stuff from them since around 2000, really good software and highly recommend isboxer!