AWB and Auto ISO in fast moving scenes
It's a toss up either way.  On the one hand AWB may help you get better footage without needing manual correction later, but on the down side, if you end up needing any correction, it will change uncontrolled on you and will complicate the process of color correction in post.  If you don't plan to color correct in post and don't have time to adjust white balance on the fly, then AWB is really your only choice.

Auto ISO has similar problems.  It should generally do a decent job, particularly if you set good edge boundaries for the ISO (which the 5d3 does nicely), but it will shift on you and make adjusting for brightness and contrast in post more difficult.

Ultimately the shot you get is better than the shot you don't though, so if you can't operate it manually fast enough to get the shots, then use Auto for what it is there for, getting the shot you wouldn't otherwise be able to get.