The Jerk and Acceleration settings can greatly effect your printed output. If your acceleration is too fast you will see artifacts on the print, if it's too slow your prints may take much longer to complete. There is a compromise and one of the ways to tune it is to use the binary search method in the link below.
Take a look at this 3d Printer Wiki
Here are some cool Calculators
A discussion on binary search for tuning
In general you may want your acceleration to be somewhere between 800 and 1250. Your jerk should be somewhere between 7 and 10. Experiment and see what gives you the best results.