there are 3 ways to use the liquid - dripping onto the atomizer, topping off your cart, or refilling your cart.
can top off cart by dripping on it. Can refill by adding some under the wadding and then dripping on top of the wadding.
I'm still pretty new at this (coming on 3 weeks of use) but what i've been doing is dripping on the atomizer for short use, topping off the cart (by dripping on it) for longer vaping sessions. I also drop a couple of drops on the atomizer when I top off a cart (but that's because I tend to vape until the cart and atomizer are both pretty dry).
So far I prefer dripping on the atomizer and using no cart (simply the empty mouthpiece), but for convenience I often use the carts (and topping them off).
edit to add - if you want to get rid of flavor in cart and use your juice instead, can remove the wadding with tweezers, rinse well, dry thoroughly (can press between paper towels repeatedly) and then fill cart. I dont have the link handy, but you can find youtube vid showing how to do this.
also, be careful not to flood atomizer when dripping (flooding can result in killing your battery). If you do, remove it and blow on end that battery connects to, and then tap the other end against jeans, paper towel, etc to remove what you blew out.