It's not necessary to have multiple copies of mIRC.exe, simply add the following to your mirc shortcuts:
-rC:\config\mirc
Put in a new directory for each mIRC. If you just want to load a new mirc.ini, not the entire dir, use -iC:\config\mirc1.ini
-r does the following:
Sets the data path where mIRC saves mirc.ini as well as other files and data. If -r is specified without a path, the path is set to that of the mIRC executable.
/help Command Line shows you all the details.