Whenever I cruise new waters, I do lots of research and purchase cruising guides and charts, if available, long before I head out. The route you are describing is pretty popular with cruisers so I imagine guides and charts will be easy to come by. I plan fuel stops around having at least 1/3 of my fuel available, just in case. I use a Lowrance LMF-200 gauge with a fuel flow sensor and a speed sensor on my boat that provide real-time MPG and range numbers as well as an extremely accurate fuel gauge so I am never unaware of my real fuel situation. Additionally, my chart plotter allows me to enter fuel use and predict range based on the route I created. All these electronic tools cost me less than a grand 11 years ago and have been ridiculously great investments... I know that in absolute worst-case situations, my boat will get at least 2 MPG and has at least a 100 mile range before I'm down to 1/3 of a tank.
There is no need for you to stay out of shipping channels on your route, in many places in the 1000 Islands it would be unwise to leave them without good local knowledge of underwater hazards (there are countless underwater hazards there). Just stay away from ships; they are pretty easy to spot, being big and ship-shaped and all... I would strongly advise you to get a VHF radio and keep it on channel 16 while cruising in shipping channels. That way they can contact you if they spot a dumb move.
Do not worry to much about this trip you have planned. It will not be terribly challenging and will be a blast. Do make sure you have your passport and the proper numbers to call for both US and Canada Immigration and Customs. They are both easy to deal with but can be nasty if you break the rules, from what I have heard.