Well, here's what I've worked out. Since I'm heading for Sgr A* right now, I type the name into the search box, then select that when it pops up. Use the little arrow by current system box to zip the screen back to where I am. Wiggle the view around until I can see the destination system. Then click on a star that looks farther away from the current system, and nearer the target. Just click on it, don't select it. The view zooms forward some (usually only 30 ly or so). Then pick another star and zoom forward, then another, etc until you're just under 1000 ly away, select the new star and plot a route.
Also, write down the intermediate target so if you get disconnected you can just search for it and re-plot your route to there, instead of starting all over.