IS Boxer has an addon in the background, which does a bunch of things for you.
As long as the addon is enabled on all toons, and everyone has unique modifiers for FTL (which the wizard does for you automatically), it will work out.

When I push a given key, the Toolkit might show this procedure:
- Hotkey: 1
- One Step
a) FTL Assist Me
b) Send 1 to all windows.

The FTL Assist Me, is something the addon does.
It will send F11 to all windows, but add the FTL modifiers for that character.
Which tells all of the others, the Assist Me originated from this specific window.
So the assist me should act like an /assist thatspecifictoon command.

You can use Alt, Shift, Ctrl etc modifiers freely elsewhere in your set up.
You just don't want to tie those to the specific few keys IS Boxer uses for FTL functions.
I believe these are F11, F12 and backslash.

I use "1" and "Alt + 1", along with several Alt + Key, Shift + Key and Ctrl + Key commands as hotkeys.
The FTL Modifiers don't get in the way of those keys working.



There is a quick start guide.

Basically, run the wizard and you're set for a basic configuration.
Most of the examples in this guide, run you through changing things in specific ways.
While many of the features are standard to IS Boxer now, the examples are still good in that they show how something works and understanding that lets you customize to your hearts content.

The IRC, isboxer.com forums and this forum will get you a lot of support too.
The basic set up is quick and easy.