A) I thought that it was possible but I do not know how to do it.
Look at /help /server
The -m switch creates a second server window.
Also in Options > Connect there is a checkbox for "New server window"
B) I have one MIRC copy loaded now. The programs are in c:\Program Files(x86). The MIRC is configured and works fine. This is MIRC #1. As far as I can tell I have permissioned the Program Files(x86) directory to allow anybody in the world to enter. Win7 makes it harder and harder to get into directories even if you are an administrator. However, the active mirc.ini file is located in the Users\Steve\AppData\Roaming Directory.
I have no clue why it defaults to that directory.
In Win7 you do not have access to the Program Files directory. Instead, Win7 uses the location AppData\Roaming when a program tries to write to that location.
So my initial assumption that both your mIRC copies are using the same mirc.ini file is probably correct.