Start here >>> http://www.canals.ny.gov/index.shtml
The whole canal system is 525 miles long, but that includes spurs like the Cayuga-Seneca, Champlain, and Oswego canals, but I believe the Erie Canal proper is something like 300 miles long and runs from Lake Erie (Niagara River just north of Buffall) to the Hudson River in Albany. The Canal Corp. says to budget at least 5 days to cruise the whole length, but I suspect that's moving along at the speed limit, which varies from 5 mph/no wake to unlimited on open river stretches.
Lots and lots of small towns along the canal, most with facilities of some sort. Fairport is one of the best, and transients only pay $7 per night for a boat the size of the Macs, and that includes water, electric, head with showers, and pump-out. Pittsford next door has no dockage fees that I'm aware of, but also no utilities or facilities. But there are restaurants. People also tie up at the locks, which all have 99 year old bollards* big enough for freighters, especially if they get there too late to lock through.
Start with "The Cruising Guide" from the NYS Canal Corp. Also, use the Active Captain web site (sign up for free - it's worth it
), which has boater comments and reviews on towns, dockage, facilities, and so forth. There is a fee for using the locks, and you aren't going far without them, but it's pretty cheap for either a season or a 10-day pass. The price goes up at 26 ft LOA, but my registration says 25 ft (probably because NYS doesn't bother with inches on the registration, and the boat is 25 ft 10 inches), so I get the middle rate (they check the reg. when you buy the pass, so you can't cheat on LOA). Unlimited bridge and lock operation with the pass. Use a hand-held at low power for bridge/lock operators, though you shouldn't need a bridge opening even with the mast elevated over the cockpit.
If you bring your mast, you can take a spur either north into Lake Ontario, or south into Cayuga Lake, or turn west just before Cayuga, through Seneca Falls (supposedly the inspiration for Bedford Falls in It's A Wonderful Life) into Seneca Lake. One of my sisters lives a stone's throw from the docks in Seneca, and one of these years I need to motor out to there, then spend some time noodling around Seneca or Cayuga Lake (the two largest Finger Lakes). It's probably a 2-day trip for me, launching in Fairport (west of town) and boating to where she lives. But this summer I'm headed off to Cape Cod for a week, so probably not this year.
Cruising the canal system is like New Year's Eve in Times Square - something you do once for the heck of it, but most don't do it a second time. Many Great Loopers use the canal system instead of Lake Ontario, in fact. It's certainly more boater friendly, as you can stop almost anywhere, and cities and towns are relatively close to each other. And it's shallow - you can drop anchor almost anywhere, as long as you're not in the travel 'lanes'. Very little current in most places, though it can get brisk when they fill or drain a lock, and of course, in the rivers, which were incorporated whenever possible to minimize the amount of excavation. The Genesee River is part of it, though it merely crosses the canal, and you can (and I have) boat right into downtown Rochester and tie up (before going over the falls
).But this relates to the OP's topic in that you spend days trailering with the boat to get there, and days on the Canal, and you'll want to use your Waterbago with the mast down the same way you'd use it with the mast up. But you do have to do something about a masthead (steaming) light. And an anchor light, if planning on hunkering down on the hook somewhere. But those are handled easily enough.
*I believe next year is the 100th anniversary of the widened and rechristened Barge Canal System, though it was first opened in 1825!.
But others here have done it, or most of it, so it's perfectly do-able in a Mac. And it would hit a lot of the places you want to try. 
But I digress.
