That puffer will eventually eat your BBGs & will attack the dragon goby too. You have to do your own stirring of the sand & then skim off the top for detrius, when you syphon for WC.
my puffers dont mess with the dragon goby, however mine are in a 55 gallon tank and the puffers stay to one side and the goby stays to the other, i also have knight gobies in there, but all are peaceful in my little glass neighborhood.
In my 250 gal brackish(1.008) tank an army of swamp ceriths (Melanoides tuberculata) seem to keep the sand in good condition. At least I have never noticed any problems with it. The sand is 1-1.2 mm grain.
Fiddler crabs do a good job of cleaning the sand. There was a very big difference in my tank after only having him in there a couple of days. Plus they are docile and as long as you give him a hiding spot for molting should withstand the puffer. On top of all that they make a nice natural addition to your tank IMO.
Currently I keep 3 flounder with my juvenile GSP. I know he might go for them someday but for now he ignores them (also they are fast- faster than kuhli loaches!). The flounder stir the sand very well and clean up whatever the GSP doesn't eat.