I only have one tank running but when I had many I must confess to using the same equipment across all of them
I so rarely have to quarantine a fish but when I do need to separate one, for whatever reason, I set up a small tank on the coffee table and fill it with water from the main tank plus a filter I have had spare kept from the main tank. Like Alan, if it was to medicate a fish I would not use a filter but if I was separating, say, some fry, then I would add the filter I had prepared earlier (cooking joke).
Once the tank is fiinshed with, the water goes on the garden and pot plants and the filter goes back in the main tank. If it was with a sick fish, I would thoroughly clean the filter then sit it in the sun for a few days but, as said, I don't use a filter with sick fish. If the tank had been infected with whitespot you only have to keep the filter away from live fish for a couple of weeks and the cysts etc will die from lack of a host anyway.