First: why do you need multiple copies of mIRC? mIRC handles multiple servers just fine, you know...
To answer your question though: use multiple configurations. You can create separate mIRC directories and launch your second mirc.exe instance with commandline switches (-r, specifically) to use that directory instead of the default.
See /help command line for -r and other potentially useful switches.
Also an option: copy mirc.exe to another directory and place an mirc.ini file inside of that directory (it can be an empty file, mIRC will fill it with defaults). Managing separate installs, executables, etc., might be easier, depending on how you use your computer.
