It can be a bit troublesome but very possible. From the galaxy map be sure to select your target world and decide/select if you are going to take the fastest route or the most economical route. I then rotate the camera to get my beginning point and end point lined up visually so that I can zoom in and watch as the jump connections are made by the computer. I then find the furthest system that is connected with a jump line and select that system as a intermediate point. Sometimes when I do this, the computer will make more jump line associations and you can add a couple more jumps into the equation. Generally, I can get to about 80 to 90 ly before I have to do it all over again.
It really comes down to getting comfortable manipulating the galaxy map. Spend some time with the controls and that will help out big time with figuring out how to plan a really long trip.
Hope that helps. If it doesn't, do some searching on youtube. Im guessing there may be a few videos out there.
Cheers,