It will be a matter of taste, rather distaste. The eel and the puffer fish are very intelligent fish. The puffers use sight and will learn quickly that eels apparently taste horrible, and your eels, being almost blind will learn what tank mates it can and can't eat.
My eels all "tasted" the puffers that resided with them and even though it is horrible to see eels with teeth bite the puffers, they quickly spit them out. The puffers skin is tougher than it looks too, because they didn't seem affected by the taste test. Soon after that though, the eels would still nose up to the puffers but would never bite at them.
The puffers also never bothered to even try to test the eels. It could be an innate or unnoted warning the eels put out that prevent them from being bullied, even by fish that could possibly consume them. The larger fish in my tank, the Datnoids would only push them around and it was funny to see the two species wrestle each other for cave space, but no harm came to either fish.
In the worse case, you'll learn very fast if your fish will cooperate.