I would put him in the breeder box for tonight if possible that way when you setup the qt you don't have to chase him down and stress him out. I would use a mix of water from your tank and some fresh saltwater so the nitrate load isn't as high but not low enough to shock his body, and do a slow acclimation when you put him in. If you have extra filter media on hand from your tank you can use it to cycle it immediately and I would throw in some decor or rocks so he has a place to hide and feel safe. PVC pipes or elbows work well too.
Then I would observe him the first few days and hold back on feeding and dosing meds the first full day in QT. Kanamycin, erythromycin or metronidazole would work well as meds if this is a bacterial infection. Foods like brine mixed with spirulina, or daphnia will help if there are any internal blockages causing this. If he refuses to eat try soaking it in garlic juice for 10 mins before feeding (works well on picky eaters/sick fish). Also make sure to take out any leftover foods if they are not eaten within 15 mins so they do not foul up the water.