I've been using the same route for practice, and I'm tiring of having to input the same waypoints every time, I use Flightsim commander, which now says it can save axe flight plans, however, any attempt at saving a flight plan, the flightplan comes out all messed up in axe. Half the waypoints go missing and the rest are all messed up to the point that its not worth saving a flightplan in fsc I can't figure out how to save the flightplan in the aircraft itself, does anyone have some help?

There's a program at Aerosoft called ConvAXE which converts FSC plans to AXE coroutes. I don't have FSC so haven't tried it.