Maybe you did not know that you can edit the flight plan to make it go any where you want. All you have to do is to click on any of the waypoints shown on the route that will bring up the map and you can add or delete waypoints all you want. You do not have to fly the route the planner picks 8). If you use IFR routes ATC will let you know when to descend. For long legs like what you want I recomend that you fly IFR and not VFR otherwise you will be constantly changing transponder frequencies. You can also change the altitude to what ever you want. As long as you use IFR ATC will not let you fly into a mountain if you are to low. And once airborn you can always request a altitude change.
So why do you need another planner for.  8)