Renaming windows in isboxer possible?

So when you run World of Warcraft normally through launcher, the window name is:
World of Warcraft

However, running it through isBoxer obviously renames the window or windows to something like:
Window 1: is1 (Ctrl+Alt+1) John-Icecrown - Trinity
Window 2: is2 (Ctrl+Alt+2) Brian-Icecrown - Trinity
and so on....

Is there any way to change the name of each window/instance in isboxer?

Yep! Open up IsBoxer Toolkit, open your character set, pick a slot, and under the switching tab, there's a toggle "custom window title".
You can do what you need to do there.