My brother, a friend and I built a raft in 1980 and did as much of the river as we could (Keokuk to below Memphis). It remains one of the high points of my life.
Be careful- the river will do most of the work for you but doesn't forgive mindless mistakes and neither do the tow-boats. With a canoe, you should be mostly out of the channel and tugs/barges shouldn't be much of an issue but they will be there and you will have to interact with them, especially while locking through (unless you portage the locks?). Another thing that snuck up on us was that the river changes personality above St. Louis where the Missouri dumps in (effectively doubles in speed). No big deal as long as you're aware of it- the river 'looks the same' but acts completely differently. Again, shallow draft of the canoe and operating in slack water will help. One other thing (based on 1980 info- likely to have changed???), on the lower river (below St.L) there are no more locks and far less places on the river to stock up/resupply. Be aware....
Have an awesome trip!