I'll go ahead and recommend trying out the ISBoxer 41 Beta.
http://isboxer.com/wiki/ISBoxer_BetaThe new Quick Setup Wizard in ISBoxer 41, when you pick Path of Exile, sets up some Hotkeys for you (called "Hold to Control Slot __") just like the ones you are trying to set up following those instructions. All you'd have to do is install the Beta, clear your profile (File, Clear) and run the Quick Setup Wizard.
But... here's my revised list of steps based on what you've posted:
1. In the top left pane under Key Maps, select Always On (I guess this is 2 steps in the guide you're copying)
2. In the bottom left pane under Mapped Keys, right click "Activate Repeat" and select "Make copy" from the menu
3. Right click your new Mapped Key which is called "Copy of Activate Repeat" and select Rename. To match the screenshot you'd name it "Activate Repeat 1"
4. Expand your "Activate Repeat 1" so under it you see Steps, 1 and 2
5. In the bottom right pane, you can set the Hotkey for this, change it so it's not the same as Activate Repeat
6. Click on the 1 under Steps
7. In the bottom right pane, under "New Repeater Target", choose the character you would like to control from your main screen (e.g. "Character: MyGuy" or "Character Slot:1 (MyGuy)")
8. Check "Block buttons from originating window" -- this is what makes it so it wont control the current window, just the other one at the time
9. RINSE AND REPEAT, FOR EACH WINDOW YOU WOULD LIKE TO CONTROL FROM THE MAIN, WITH A DIFFERENT HOTKEY