What kind of Puffer? Most do not handle a lot of flow. It tires them out. That's not what any animal wants when they are sick.
What temperature is the water. Water at 70 can hold a lot more O2 than water at 80. Unfortunately, most QT discussions about the Ich parasite want us to raise the temp to speed up the parasite populations life cycle, thereby speeding up their demise.
What is being used to treat this Ich and how long has it been going?
Has Garlic Oil (see my best treatment for Ich in the Reefkeeping Tips, linked below) been used in the feeding?
Honestly though, by the time a fish is breathing hard, it's usually past the point where elimination of the parasite matters. It may already be succumbing to the more devastating effect of a bacterial infection, brought on by the battle with Ich, often fatal. Sorry. I believe that Parazipro is sometimes useful for bacterial infections.
Aloha,
Mark