Yea you're right I actually do have a section in the script where it grabs the 2 instances of WoW and assigns 1 as the main and one as the clone:

I'm just gonna post my script so you can see what I'm working with:

Code:
; For Dual-Boxing World of Warcraft
;    by Rests (aka Eskimz)

;--------------------------------------------------------------------------------


; // Tell user what is about to happen upon start-up //
    SplashTextOn, 250, , Preparing to find your Main and Clone windows of WoW. 
    Sleep, 250
    SplashTextOff 


; // Grab unique window IDs //
    WinGet, wowid, List, World of Warcraft




; // Minimize All WoW windows //
    WinMinimize, ahk_id %wowid1% 
    WinMinimize, ahk_id %wowid2% 




; // Determine Main and Clone Windows //
    WinActivate, ahk_id %wowid1% 
    MsgBox, 4, , Is this your WoW Main window? (press Yes or No) 
    IfMsgBox Yes 
        idMain = %wowid1% 
    else 
        idMain = %wowid2% 


    If idMain = %wowid1% 
    {
        idClone = %wowid2% 
    }
    else
    {
        idClone = %wowid1% 
    }


; // Activate All WoW windows //
    WinActivate, ahk_id %idClone%
    WinActivate, ahk_id %idMain%




;--------------------------------------------------------------------------------


; // Defines the ClonesPush function //
    ClonesPush(strKeys)
    {
        global idMain
        global idClone
        IfWinNotActive, ahk_id %idMain%
            ControlSend, , %strKeys%, ahk_id %idMain%
        IfWinNotActive, ahk_id %idClone%
            ControlSend, , %strKeys%, ahk_id %idClone%
    }




; // Defines the ClonesClick function //
    ClonesClick(strKeys)
    {
        global idMain
        global idClone
        IfWinNotActive, ahk_id %idMain%
            ControlClick, , ahk_id %idMain%, , %strKeys%, NA
        IfWinNotActive, ahk_id %idClone%
            ControlClick, , ahk_id %idClone%, , %strKeys%, NA
    }




;--------------------------------------------------------------------------------


; // Hotkeys // 


    *^l::Suspend                                ; //  Ctrl + L        Suspends AHK
    ~!Tab::
        WinSet, Bottom, , A
        return




; // WoW Hotkeys //


    ~RButton Up::ClonesPush("=")                        ; //  RClick Up        Interact w/ Target


    ~^WheelUp::ClonesPush("-")                        ; //  Ctrl + Wheel Up    Interact w/ Target


    ~r Up::ClonesPush("r")                            ; //  r
    ~r::ClonesPush("=")                            ; //  r


    ~+g::ClonesPush("{Shift Down}g{Shift Up}")                ; //  Shift + g        (Follow)


    ~Space::ClonesPush("{Space}")                        ; //  Spacebar        (Jump)
Should be easier that way so you have more information.