So we just had ours. It went surprisingly well. A couple of points:
1) It requires organization and planning to be effective. Exactly what, where, who, is to be audited? Pre-submitting documents helps a ton.
2) Doesn't require as much "babysitting" of the auditor. Ours did a section of the audit, then we disconnected while he did his write up. Then did another section. Rinse and repeat. I didn't feel like I had to poke into the conference room to make sure everything was moving along.
3) Find a good platform. You probably want some type of mobile option, so you can show things out on the floor if needed. We used an Ipad which worked well. Also, a platform that you can share screens on would be helpful. A lot of "documents" are now spreadsheets and the like. It's easier just to open it up and share your screen with the auditor. We used skype and had to try to show some docs via the camera -- which was a little more difficult.