(Updated with instructions)
el Capitan is resetting the outgoing SMTP server when you upgrade if it is one of the common accounts when you setup (Google, Hotmail, Yahoo...).
I saw the same problem two weeks ago in the GM beta release (and reported it), installed the release GM last night, flashing if anything is in the Outbox.
I have a few domains forward all email to a single gmail account where their spam filters eliminate 95% of the junk. My OS X Mail retrieves the email from that account and nicely shows what email account it was originally sent to. That part still works under OS X 10.11
When I send email, I use the original ISP SMTP server, technically Gmail will send email using your email return list, but good spam filters will notice that the email isn't coming from the same domain as the listed return email address, and give negative spam points.
On each email account (domain), the new Mail app retrieved email correctly, but the Sending SMTP had been reset to gmail with the wrong ports and no password. Result: flashing message window whenever the Outbox can't send a message. What an annoying interface that is, especially if you are working on another email.
You have to edit the Outgoing SMTP parameters in a separate window. Get the parameters from gmail or yahoo setup, enter them in Mail -> Accounts -> Account Information - > Outgoing Mail Server (drop down menu) -> Edit SMPT Server List -> find the service parameters that need changing ** n.b. Apple resets to SSL because that is gmail, that may not be your server.
Mail used to allow you to change the sending server (email address) if the first attempt doesn't work. At least on my installation, I can't change that anymore - I must delete the email - OR drag it to another mailbox - until the configuration is fixed.
Seems a point release is coming soon for el Capitan, but that will only help people upgrading in the future....
JF