If you want to use only wifi, you would leave the switch on and put the controller wither before teh switch (better) or after it (likely easier).
If you put it before the switch, you can have the controller on but the switch would still turn them on and off (as would wifi). After the switch, would work much the same, but turning the switch off would likely require turning on the switch and turning on by wifi (the controller would loose power and would either revert to it's default state or remember last state, realy depends on the internal design of the controller).
All the controller is is a wifi controlled switch. So you are in effect putitng two sitches in series.