Neomycin is not absorbed through the digestive tract, so all you will do by adding it to food is kill the bacteria in the gut. If you kill enough of it you will kill the fish. If you add it to the water it will be absorbed through the gills and will act systemically. However I'd skip the antibiotic unless you have some indication it it required. It is not something to be taken lightly.
Puffers tend to drift about sometimes when they are sleeping and this can happen, I've lost one this way. There is really nothing you can do but wait.
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