Trevor, for you unit set it to 70% as a starting point. The unit will go through a series of tuning moves and will usually end up pretty close to where it does when you do a manual tuning. You should tune it while the MoVI is being held or mounted the way you plan to operating. That will get you the highest settings.
I'm sure that Brad or someone can jump in here with a really great, and more accurate explanation, but think of it as a user-defined variable for how stiff the motors will be tuned to. A higher percentage produces higher tuned results, but also a higher likelihood that you will have oscillations during normal usage. A lower percentage produces lower tuned results, and while it likely won't cause oscillations, motor performance won't be as good. For caged MoVIs, such as the M5 and M15 (or the M10 with the cage upgrade), the recommended percentage is 70%. For the classic M10, or configurations with the top of the cage removed, the recommended percentage is 50%. My normal practice, when I choose to use autotune, (with the M15 caged) is to tune to 75-85%, then manually find which axes are oscillating, and manually turn them down.