First of all, I'm still using mirc 6.2. I'm currently trying to get used to the treebar, which is unfortunately proving to be difficult.
Are you using 6.2 only because you don't like the treebar? If so you could just close the treebar via the view menu.
I don't think there is a way to custom group windows, but you could use the -z switch when creating the custom windows so they will always be at the bottom of the treebar and always at the end of the switchbar.~ Edit ~
Riamus2 beat me to the -z switch.