Using water from your DT is great as long as you have confidence that it doesn't have parasites or disease. It's Ok to use Prime with a chelated copper like Copper Power or Coppersafe. It's not safe with ionic coppers like Cupramine or Brightwells.
Consider adding a mesh bag of ceramic media like Seachem Matrix or Fluval Biomax to your HOB. Soak both the foam filter and the mesh bag with something like BioSpira, Seachem Stability, etc. for a few hours. Can pour the leftover liquid into the QT.
Adding a foam bubble filter where you soak the foam pad the same as above will help a lot to cut down on water changes.
I leave a set of all of the above soaking in my DT sump all the time. Builds a great colony of bacteria on the media.
I've treated puffers with copper. Copper Power to be specific. There was no sign of parasites so I slowly, slowly, slowly raised the copper levels over 5-6 days, always watching for bad reaction to the copper like suddenly stopping eating, lethargy, etc. Small doses spread out throughout the day. Really small doses.
Make no mistake, puffers have a history of not doing well with copper. It's much safer to use CP.