Further research, it appears the default C172 with the 540 GPS doesn't require anything special, I can rubber band a course on the map, add in way points in the flight plan, etc and it all works great
The C172 with the G1000 I have the exact same issues I've had in other planes with a G1000, first way point and the GPS clicks off, I have to press NAV again to get it to follow the magenta line...