For one you have to watch what the state maps are telling you and what they are not telling you. In Minnesota they don't tell you the shoulder is 4 foot wide but all but the first six inches along the white line are nothing but rumble strips...aka their is no shoulder to ride on. The MN state bicycle maps don't tell you that, you learn that when you go there and ride and have nice traffic volume with 25-45 mph cross wind while being on the downwind side of the traffic and you are also now dealing with no shoulder to ride on.
For me, I decided where I am going to ride to, hope on ridewithgps and point and click and the on the start and finish point and let ridewithgps decided the shortest route. I may tweak it a bit trying to find a less hilly route while still keeping the mileage down. I may also tweak it if I know I have to stop in a particular location. Otherwise I just ride the ridewithgps route. I don't mind riding with the traffic. In 18,000 miles of cross country travel I have not had any kind of trouble with cars at all. I ride the highways and generally federal highways all the time. I don't worry about the small stuff...then again it is all small stuff. It does help that I am sitting right not at just under 124,000 miles of on road/pavement biking since mid-May 2011. I'm used to riding with the traffic thanks to riding in NH where the traffic never stops.