On the Explorer and the NT, I dedicate(d) the smaller pannier for tools, tire gauge, slime tire inflator, rok straps, rain liners, first aid kit, gorilla tape, stop-n-go worm plugs, a rag, bike half-cover, etc. Basically things I want with the bike all the time. I wasn't lucky enough to receive a tool kit with the NT, but the Explorer did come with one - I do keep that under the seat since there's a spot specifically for it.