Wormer plus is apparently beneficial to filter bacteria. I do know it doesn't harm the filters at all from personal experience and I wouldn't use it if it did. The quiet puff with the sunken belly...does its belly seem to grow big when eating then sink in rapidly afterwards? If so then worm the tank as it won't harm the other two when using wormer plus. Just make sure you don't have snails in the tank (or shrimp) as it will most likely kill them.
How planted up is the tank? Are you testing daily for parameters seeing as the tank is nelwy cycled? The wormer plus won't harm a new or old tank. Puffers are very sensitive to anything but perfect water conditions.
I feed my puffs on live (and frozen) bloodworms. They also get vitamin enriched brine shrimp and mysis shrimps and snails the same size as their eyes. Snails like ramshorn and pond (bladder) snails are suitable and to be about the same size as their eyes if they are going to have any chance of eating them whole. If ou have slightly bigger snails just crush them lightly between your fingers.
Your tank size is fine for 3, but no more. An oversized filter is necessary for puffs as is a large weekly water change
The key to feeding without making a mess is not to overfeed. Rinse out the frozen food before feeding and use a pipette to feed so you don't put in too much. I don't know what the things are in the substrate are that your puffs are eating.
A worm cone feeder is good for feeding live bloodworm as it keeps them in one place.