A few things.
[A Shaw-Fujikawa Translight Engine] remains active for the entire period that a spacecraft is in the slipstream. - Halo Wiki
Human Slipspace velocities are ... approximately 2.625 light years per day - Halo Wiki
In addition to temporal anomalies, UNSC ships aren't able to jump with exact precision. A ship may transition back to normal space millions of kilometers from its intended destination. - Halo Wiki
So, let's say you want to travel 13.125 light years to a star. You turn on your drive, enter the Slipstream Space, and proceed in the direction of the star for 5 days. Then you turn off the drive and you exit Slipstream Space. You know when to exit because you know the distance you want to travel and the average time it takes to cover that distance while in Slipstream Space.
Because of the time distortion that results in Slipstream Space, you don't usually emerge exactly where you want to go. So you expected to have traveled 13.125 light years, but maybe it is more like 13.12497.