I haven’t found a way to create a VFR flight plan in Navigraph like I can in Skyvector.
For flight plans in general, there are two types of waypoints, fly-by and fly-to. Fly-to means that the flight path goes over the waypoint before turning. Depending on the speed and the angle of the turn, the aircraft will not be exactly on the flight path while turning. Fly-by means that the flight plan goes by the waypoint while turning always keeping the aircraft on the flight plan. The aircraft goes NEAR the waypoint, not OVER. The best example of these is flying at an angle to an ILS via the IAF. Fly-to means the aircraft flys over the IAF and localizer then turns back to intercept the localizer. Fly-by means the aircraft starts turning before the IAF and intercepts the localizer without flying over the IAF.
Unfortunately, I have not found out how to designate fly-by or fly-to for a waypoint.