Once you click the target where you want to go, zoom back to where you are while not unclicking your target destination. In a small bubble around your ship on the galactic map, you will routes to different star system in blue lines, the game determines the best route for you by replacing blue lines with orange ones. The only thing is, you have to memorise the systems you need to jump too as it does not save, and then recheck once you get too the end of your little bubble to re-plot the route. Hope I helped CMDR. You will see what I mean by the little bubble and routes when you look at the galactic map
But I may be wrong, as I've never used it too plot long distances, as I usually see an area I want to get too far away, but explore while heading there, but when plotting courses close to me, as I stated above happens.