I always follow the general rule NEVER to activate any switch that carries signal during a performance. The reason is there may be a different voltage potential on one side of the switch compared to the other side. When the switch is activated this voltage surges and creates the pop. The foot switch is usually protected by the !M resistor at the beginning of the circuit which bleeds off this voltage. If you still have popping from the foot switch, it mat be mechanical noise from the switch itself.