(MacBook Air, mid 2013, new install on wiped drive of OS X 10.11 El Capitan)
According to "Internet Accounts" preferences, I have five active email accounts: iCloud, gmail, yahoo, americtech.net, and Comcast. I thought I had set up Mail.app, but found only two accounts were listed: iCloud and Comcast. When I attempt to add an account (any of the remaining three), I am asked for username and password, then informed that the account is already active. Mail.app has not crashed, just won't accept any other accounts. I have all five running on an iMac (Yosemite) and an iPad.
No apparent way of manually setting up the accounts; I'm thinking of visiting the Genius bar!