Okay, so, I tried all day to set a simple Custom Arrival EndPoint. As reported elsewhere, you could just type any co-ordinate you want or just click on the map and set it as arrival.
But, once you begin flying, the game seems to forget that the arrival point was set. At least for me. It does not matter what other settings of VOR/GPS guidance everything is turned on.
The Solution.
Set both the Departure and Arrival to the same Airport (near which you have your custom location). Then, enter your custom location (with the search box or just click on map), and ADD.
Now, the navigation aids show your custom location so you can actually find your local landmark or house or whatever it is that you are flying to.