Let's say you want your new default directory to be C:\default and your mIRC.exe is here: C:\mIRC\mirc.exe.
Then you create a shortcut with the following data:

(Sorry, that text is in German, but I guess my point is clear.)
If not..
//run $mircexe -r"C:\default"
If you type that in mIRC, you will run a 2nd mIRC with C:\default as your default directory, where mirc.ini and such will be stored...