Sure. Any key you wish to have HKN "hold" while you keep the hotkey pushed needs to be defined as a movement key, instead of a normal hotkey. http://hotkeynet.com/p/movement.html

you actually have some movement keys defined in the script:

Code:
//-----------------------------------------------------------
// DEFINE HOTKEYS FOR ALL FORMATIONS BINDS.
//-----------------------------------------------------------
<MovementHotkey ScrollLockOn 8>  
<SendLabel w1>
     <Key F1>
<SendLabel w2>
     <Key F1>
<SendLabel w3>
     <Key F1>
//-----------------------------------------------------------
// DEFINE MOVEMENT KEYS THAT WILL GET SENT TO BOTH WOW'S.
// ADD MORE KEYS IF YOU WANT.
//-----------------------------------------------------------
<MovementHotkey ScrollLockOn W, A, S, D>
<SendLabel w1, w2, w3>
<Key %Trigger%>
The latter part means that your WASD keys are always benig broadcast to all 3 windows while your hotkeys are active and scroll lock is enabled. This is generally not how multiboxing in WoW works and people use /follow to move around, so unless you have some specific reason to be doing it this way, I would advice changing/removing that part.