I've seen people do UWorld every way possible and I don't believe how you go about it really makes a difference in the end. I do think if you wish to do it random timed, you should already have a good grasp of the material in FA. Otherwise you're going to get a lot of questions wrong simply due to forgetting simple details. I've seen a lot of people really benefit from doing it subject / organ system wise, particularly those who did it relatively early on in their prep. I've even had friends switch from random to organ system and they benefited from it, the general idea being to go through an organ system and then immediately reinforcing it with UW.
If you're planning on doing it 2x, you have the option of going organ-wise the first time around, and then random.
