You need to rename your two windows and then label them before you do the HoldDownKey as shown in the Quick Start Guide

Step 4. If you're running more than one copy of WoW on a single PC, make a hotkey to rename their windows. For example, if you have two PC's with two WoW's each, you'd write something like this:

<Hotkey Ctrl R>
<SendPC local>
<Rename "World of Warcraft" wow1>
<Rename "World of Warcraft" wow2>
<SendPC 192.168.1.102>
<Rename "World of Warcraft" wow1>
<Rename "World of Warcraft" wow2>

Step 5. Make a mailing label for each copy of WoW. Use SendWin for windows that always stay in the foreground. Use SendWinM for windows that sometimes or always stay in the background. For example:

<Label Joe Local SendWin wow1>
<Label Sam Local SendWinM wow2>
<Label Sue 192.168.1.102 SendWin wow1>
<Label Meg 192.168.1.102 SendWinM wow2>

Step 6. Define movement keys that make all your characters move when you hold them down. For example:

<HoldDownKey w, a, s, d, up, down, left, right>
<SendLabel Joe, Sam, Sue, Meg>