In Just Learn Morse Code, and I suppose other programs for learning and practicing Morse code, Farnsworth timing is option (just as using Koch's method is an option).
Farnsworth timing is controlled by using two numbers for speed. If the two numbers are equal, you're using standard timing. If the numbers are different, you're using Farnsworth timing.
The Just Learn Morse Code help file contains some information about Farnsworth timing. You'll find it in the help menu.