You could drop the 6" pots into some much larger pots (perhaps 12" dia), with some more pellets filling the space between the pots. This preserves the ability to move the plants around easily, as opposed to filling the flood tray with pellets.
You might put a 6" depth of pellets in the 12" dia x 12" tall pots before filling in around the current 6" pots, but make sure your taproots get down to the flood level when potting up. Hand watering for a few days will help encourage the roots to seek the flood level.