Hey Don,
The Boundary Waters are pretty darn cool, and Quetico is even nicer. I went a couple times as a kid, but when my wife and I started going, we just went to the library and got one of dozens of guidebooks (pre-internet days) and picked a route and tried it. Since then we've been several times, trying different routes and areas, so we had a pretty good idea what we were getting into when we first took Grace. I am sure now if you search the web, you will find more advice than you ever wanted on picking routes, and would just have to sift through it.
As far as the trip with Grace, she had been out rowing and canoeing with us since she was a few weeks old, and car camping almost as long, so , again, we had a pretty good idea how things would go. The first year we picked a lake about a half day's paddle (under normal circumstances) in, went there and set up camp. Then we day-tripped from there, so that we were never too far from being able to bail. Last summer, when Grace was 3 1/2, we did a real loop, and she did great, even though we had a day of cold rain. We try to keep the paddles and the portages reasonably short, and the trips were really only three days in the boat, plus a night of car camping on either end. We went to a seminar a couple years ago given by a family who had done serious expeditions with their toddlers, so it can be done, but with three people and a big dog in the boat, we would have to look into a frieght canoe to go much longer. All we took special was a small fishing pole for her to use while we paddled and a couple books for the evenings, though a quick Google of "wilderness canoeing with kids" suggests that some kids need more, um, stimulation. That said, there appeared to be quite a bit of useful advice on the subject.
All that said, there are alot of great places you can go on a three or four day trip without half crossing the country. We have been to Killarney and Algonquin in Ontario, and I know there is stuff in the Adirondacks and Maine. You can go into Quetico and not see other people for a week or two, but I am not sure three-year-olds fully appreciate that. I do look forward to longer and longer trips.
Jon