Here is a snippet of some HKN code that deals with an FTL system. It's pretty basic, really. All you do is launch your 5 instances of WoW (giving them unique names like WoW1, WoW2, etc) and then ask HKN which window the command was sent for. HKN then sends whatever keystrokes you want it to (in this case it reads that it came from WoW2 and therefore appends "RCtrl Ralt" to the keystoke so all clients know to assist my WoW2 toon).

Code:
//General Sharing
<Hotkey ScrollLockOn a, c, d, f, g, r, t>
	<Passthrough>
	<If ActiveWinIs WoW1>
		<SendLabel WoW2, WoW3, WoW4, WoW5>
			<Key RCtrl %Trigger%>
	<Else If ActiveWinIs WoW2>
		<SendLabel WoW1, WoW3, WoW4, WoW5>
			<Key RCtrl RAlt %Trigger%>
	<Else If ActiveWinIs WoW3>
		<SendLabel WoW1, WoW2, WoW4, WoW5>
			<Key RCtrl RAlt RShift %Trigger%>
	<Else If ActiveWinIs WoW4>
		<SendLabel WoW1, WoW2, WoW3, WoW5>
			<Key RAlt %Trigger%>
	<Else If ActiveWinIs WoW5>
		<SendLabel WoW1, WoW2, WoW3, WoW4>
			<Key RAlt RShift %Trigger%>
	<Endif>

<Hotkey ScrollLockOn LShift a, c, d, m, r>
	<Passthrough>
	<If ActiveWinIs WoW1>
		<SendLabel WoW2, WoW3, WoW4, WoW5>
			<Key RCtrl %Trigger%>
	<Else If ActiveWinIs WoW2>
		<SendLabel WoW1, WoW3, WoW4, WoW5>
			<Key RCtrl RAlt %Trigger%>
	<Else If ActiveWinIs WoW3>
		<SendLabel WoW1, WoW2, WoW4, WoW5>
			<Key RCtrl RAlt RShift %Trigger%>
	<Else If ActiveWinIs WoW4>
		<SendLabel WoW1, WoW2, WoW3, WoW5>
			<Key RAlt %Trigger%>
	<Else If ActiveWinIs WoW5>
		<SendLabel WoW1, WoW2, WoW3, WoW4>
			<Key RAlt RShift %Trigger%>
	<Endif>


//Hotkeys for the macros that are not target specific
<HotKey ScrollLockOn b, 1, 2>
	<SendLabel WoW1, WoW2, WoW3, WoW4, WoW5>
		<Key %Trigger%>

<Hotkey ScrollLockOn Shift b, i, x, 2>
	<SendLabel WoW1, WoW2, WoW3, WoW4, WoW5>
		<Key %Trigger%>

<Hotkey ScrollLockOn Ctrl m, p, r, z>
	<SendLabel WoW1, WoW2, WoW3, WoW4, WoW5>
		<Key %Trigger%>

<Hotkey ScrollLockOn Alt m>
	<SendLabel WoW1, WoW2, WoW3>
		<Key %Trigger%>


//Follow when lead is autorunning
<MovementHotkey ScrollLockOn MButton>
	<Passthrough>
	<If ActiveWinIs WoW1>
		<SendLabel WoW2, WoW3, WoW4, WoW5>
			<Key RCtrl LShift Z>
	<Else If ActiveWinIs WoW2>
		<SendLabel WoW1, WoW3, WoW4, WoW5>
			<Key RCtrl RAlt LShift Z>
	<Else If ActiveWinIs WoW3>
		<SendLabel WoW1, WoW2, WoW4, WoW5>
			<Key RCtrl RAlt RShift LShift Z>
	<Else If ActiveWinIs WoW4>
		<SendLabel WoW1, WoW2, WoW3, WoW5>
			<Key RAlt LShift Z>
	<Else If ActiveWinIs WoW5>
		<SendLabel WoW1, WoW2, WoW3, WoW4>
			<Key RAlt RShift LShift Z>
	<Endif>