i've never tried putty w/ wow, but if the auto-add doesn't work or if you wish to utilize the maximizer, this should work:

run keyclone.
uncheck keyclone/setup/general/auto-add-windows
run your wows normally, in windowed mode.
once you are at the login screen... click 'add' on keyclone and click the middle of the wow screen
in keyclone, for the wow just added... right-click on it in the keyclone list / maximize and select the region you want to put it in (ignore if you don't want to use maximizer)
repeat for all wows

let me know if that's what you were looking for