You could try the “Kratky method”, so you could basically not use the C&G cups at all, but instead put your own net cups in the water tank holes. Place the pre-grown seedlings in a small rock wool cube. The root should have some room to breathe. Place the cubes upright into the net cups. Stabilize the cubes with a few clay pebbles or small stones. Mix your nutrition and then fill the water level up so that it barely touches the net cup bottom. When you need to re-fill the tank after a few weeks, make sure to only fill it about half the level to the net cups, else the plants can drown.
Note that this only works with the 2nd gen C&G devices.