"
I would definitely give them each their own mIRC folder; completely independant mIRC installations"
I definately wouldn't,.

Using the default mIRC install path with seperate working dirs allows for much easier upgrading. Install the upgrade once with the default path, and all users copies are upgraded.
This also allows "each of them to customize all they want with sounds and scripts and logs and downloads, without the other one complaining about changing stuff or deleting stuff".