My next try, hopefully whenever i press "C" it will set the vars on the fly ill try it when i get home.

c::
KeyWait, c, D
IfWinActive, World of Warcraft
{

; Get both ID's variables
WinGet, wowid, List, World of Warcraft
winone = %wowid1%
wintwo = %wowid2%

; Get current window a variable
WinGet, active_id, ID, A
active = %active_id%

; Make the active chrMAIN & not active chrAlt
if %active% = %winone%
chrMAIN = %winone%
chrAlt = %wowid2%
else
chrMAIN = %wintwo%
chrAlt = %winone%
Return
}