Altitudes is something that LNM doesn’t do particularly well at the moment. However, it does have a flight plan elevation profile feature that allows you to set the most suitable overall plan altitude.
At the top of the flight planning window there is an adjustable field which is used to set the overall plan altitude as well as a choice between setting the plan as VFR or IFR:
If you open the flight plan elevation profile window you’ll be able to see the terrain elevation for the route, it’ll also automatically show you the recommended altitude for your plan. With that info, you can set the correct altitude for your flight plan.