I squeeze, shake, squeeze, smack against the side of the sink, squeeze, swish around and repeat until either I don't get any more brown water out or I get sick of doing it. Whichever comes first. Back when I could be bothered testing I tested after some times I'd forgotten to plug the filter in for a couple days, power outages, etc that were long enough to presumably have killed the filter. And I never got a measurable ammonia reading. So, I think assuming you have a mature tank and aren't overstocked there's no need to worry about it. The bacteria doesn't just live in the filter, it llives on every surface in the tank, the gravel, the glass, the plumbing, probably even on the fish. So killing off some isn't going to be a big deal.