Most will just keep trolling and fight the fish. If you're lucky, you might double up. If you aren't confident with that, you can just pull everything. There are boxes out there for flashers, called "flasher files" I think. You could also just store them in a plastic bin. Flies can be hung from pool noodles upside down somewhere on the boat or wrapped around the noodle. You could also put them in small plastic bags.