If you mark the box for all data folders, it will run on all four data folders if they are on your company list under open company.  However, it can take a really long time for some companies to do it this way.  We have many archive folders and instead of marking all data folders, we do them one at a time.

Like how long, cause I just made this mistake? SMH

Really depends on the size of the files, the number of folders and available memory. 

Additionally file doctor is going to run again and again on the same "shared" files such as the Master.QLM stored in the GLOBAL folder.

Is it possible to run File doctor on main server and a second on a terminal server? at the same time?

Disregard last question? I was not in my right mind when I asked. lol Thanks for your responses. 

I see you already realized the answer is you shouldn't even try to do that even if it lets you.