Hey, I had the same problem, there was no checkbox for "Use only this server".
In addition, when I compose a new email, there was no "From" that I can choose to select.
Lastly, I couldn't drag and drop an account that I want to make as default account.
I'm using OS El Capitan, and Mail v9.3.
But, I managed to solve my problem, by going to Mail > Preferences > Accounts.
I clicked on each account that I do not want to be default, and under the tab "Account Information", I unchecked "Enable this account". This will inactivate the account.
I repeated the above step for all accounts that I do not want to be default accounts.
So the only account left active is the default account I want.
Then I went back to each deactivated account, and re-activate them again by checking "Enable this account".
Then for some magical reason, the checkbox for "Use only this server" appeared. And the "From" in composing a new email also appeared. And the composing new email auto selects my chosen default account as default. And, be clicking on the "From", I can choose manually another account to send from in my composing new email.
YAY!!