The point why the <If> statement doesn't do the trick is, that the command <If variable Is value> needs a variabe to compare, and what you are doing by <If %1% Is %2%> and calling <ApplyTemplate FTL "6" "6">is replacing the %1% and %2% with '6' so that it looks like: <If 6 is 6>. For HKN this means it has to check if a variable named '6' has the value 6. And since you have not set a value vor a variabel '6', this always fails.

Ehat you could try is first set a variable to the value of %1% and then compare it with %2%, like:
Code:
<Template FTL>
    <Hotkey %1%>       
  	<SetVar compare %1%>
  	<If compare Is %2%> 
        	<SendLabel w1, w2, w3, w4, w5>
                  	<Key %1%>
   	<ApplyTemplate SendLeaderless "%1%" "%2%" "rctrl rshift" WoW1 "w2,w3,w4,w5">
        <ApplyTemplate SendLeaderless "%1%" "%2%" "rctrl ralt" WoW2 "w1,w3,w4,w5">
        <ApplyTemplate SendLeaderless "%1%" "%2%" "ralt rshift" WoW3 "w1,w2,w4,w5">
        <ApplyTemplate SendLeaderless "%1%" "%2%" "rctrl ralt rshift" WoW4 "w1,w2,w3,w5">
        <ApplyTemplate SendLeaderless "%1%" "%2%" "rctrl" WoW5 "w1,w2,w3,w4">      
<EndTemplate>
..and you would need to change the <Template SendLeaderless> to use an <ElseIf ActiveWinIs %4%> instead of <If ActiveWinIs %4%>, because you can't nest Ifs.