How you do it is really up to you.
I've found the best way to do it is bring the water right up just barely touching the cube. Actually the best way is if the water level is just below the cube, and the air bubbles actually wet the roots, not the water.

Of course its critical that the roots get moisture, and exactly how you do it ... the plant doesn't care. You don't want it drying out, but you don't want it drowning either.

SN