We do the same thing as what we do with interplanetary travel. You use your knowledge of orbital mechanics to determine how long it takes for you to get there, and model the motion of the target body to predict where it will be after that much time has passed, and then you use this information to plan your flight.

Stars have a much more complex orbit than planets do as they are affected strongly by nearby stars and not just circling a single center of mass like planets do around stars. So you need a lot of computing power, and a lot of data about the initial positions and speeds of each star. Then because with interstellar travel we are often contemplating journeys of many centuries or even longer, you have to worry about any inaccuracies in your initial data compounding on each other. In the FTL case you’re only dealing with decades of travel, so the calculations actually require less precision than those longer slower than light trips would.