1) Open the program directory of your "second" mIRC installation (the one you want to use as a bot). It's the directory that contains the "mirc.exe" you want to start to run your bot.
2) Create a blank new file called "mirc.ini" in this directory.
From now on, your "second" mIRC installation will use this directory instead of the "roaming" directory for all it's settings and as it's "home" directory (...just ensure your windows account has write access at this directory).
You don't have to, but you may use a copy of the mirc.ini of your "first" installation instead of creating a blank new mirc.ini file - to copy all the settings of the "first" installation to the "second" (and now independent) mIRC installation.
And you may copy other files to this directory as well, like servers.ini = your server list etc. But, as stated: everything except the mirc.ini is optional, and mIRC will create blank new files if necessarry for all the files you don't copy there.