In a small ZipLoc bag. Put your scent product in the bag prior to getting on the water. When you want to apply, lay your bait in the bag and use your hand outside of the bag to work the bait around. When you're done, remove your lure and seal the bag up. Good to go.
That's the way I do it too. I also just put it in the bag of plastic that I'm using, but if you leave the scent in the bag of plastics for a long period of time it breaks the plastic baits down some. If you're going through the bag of plastics relatively quickly within a day or three you should be OK.