The tool kit goes in the compartment door, not the bag. Also, if you get any air in the tube it won't flatten out (this was my first bike with a presta valve so I made the mistake of opening the valve to see how it worked and discovered that the tube immediately sucks in some air; it took me a while to squeeze it all out again).
Ultimately, I only got one CO2 canister and one tire lever in the bag, so I carry the extras in a baggie in my jersey if I'm going more than a few miles from home. If I had the Bontrager tire levers I probably could have gotten both in, but the ones I have are too thick.