AP,
 You'll be just fine! As backpackers you have the physical skills, the paddling part will come with practice. Navigation is a little different, so make sure each canoe has a set of maps, and the night before or morning of, let EVERYONE see the route your taking, not just the guy's doing the navigating. 4 sets of eyes are better than 2. IF you unsure of your navigating with islands/ points of land, shoot a compass heading for each portage or campsite destination. If you get "confused" go with the compass heading. Make sure you "know" where you are while paddling. In new water, I find marking on the plastic cover of map case with a grease pencil when I hit a prominent landmark, helps keep me orientated.
Sometimes, especially when your excited and caught up in the scenery/fishing, you can get turned around if your not careful?
 Of course if you have/use a GPS, then it's not such a big deal.
Use the same common sense you would backpacking, and you'll have a fantastic trip and hopefully a good trip report with pics ;)