Quote; do you take the tops off or leave them on but pierce them?
Either or! the piercing method sounds best to me, a bit like a 'leaking hose' plus the water is fed higher up the plant wheras with cork off it all goes to the base of the bag/pot.
Quote; And how do you stop them clogging up?
You can't but don't worry the water will get to where you want it eventually.
Keep the top of the bottle (funnel) a few inches above soil level, aim better an you wont wash compost into the bottle / funnel to clog it.