I have a 2012 vintage 13" Macbook Pro with a hard drive, my husband has the 2012 vintage Retina display Macbook Pro with flash memory. We keep both our OSs fairly current. We don't need to be on the "bleeding" edge of technology, so not intererested in participating in any betas, but we are definitely not being dragged to the latest levels. I upgraded to El Capitan on my Macbook on Oct. 15th after I saw all the glowing reports in the media. I had no problems on mine Macbook, so a few days later, I upgraded my husband's Mac to El Capitan. He had an initial problem sending emails, but I was able to fix it by going into Mail preferences and fix the SMTP settings that the upgrade had changed. (My ISP (inmotionhosting.com) uses port 465 for SSL IMAP outgoing (SMTP) and 993 for SSL IMAP incoming and those had gotten changed to back to the usual suppects of 587 and 43, respectively. Also, the IMAP PATH had gotten blanked out, so I had to reset it to INBOX). He then went out of town and all **** broke loose on his Mac while at his client's site. He was getting invalid SMTP server error messages and invalid server certificate messages whenever he tried to send anything. He was able to receive emails with no problems. I talked him through fixing the SMTP advanced settings and trusting the certificate pop-ups and all would be fine for a few more hours before the errors occurred again. I didn't know if changing locations (client to hotel back to client) was contributing to the issue. He finally got so frustrated that I had him delete his email accounts and re-add one back. Btw, both of his email accounts are hosted in the same domain on our ISP.
Once he got back home and I was able to "drive" his Mac for myself, I was prompted about the untrusted SMTP server certifcate and I selected to "Always" trust it. (There are three different statements that has to be set to "trust", in order for it to be "always".) I unchecked the "Automatically detect and maintain account settings" in both places for the mail account, on the Advanced tab for the IMAP account and on the Advanced tab for the SMTP server. I had it unchecked on the SMTP settings but not on the IMAP Advanced panel. I haven't had a problem sending emails since. However, the mail app wouldn't stop downloading the mail. I could only guess that it was downloading the same mail over and over because his mail file has around 34,000 messages and it had downloaded over 2 million messages before I stopped it.
I tried deleting his mail account again and re-adding, to no avail. I found DeMinister's post about deleting everything in the V3/maildata folder and that fixed the continuous downloading problems. (Since I had never had to do something like this on a Mac before, I had to figure out how to get to the hidden system files in the Library folder. In a Finder window, hold down the Option key and select the Go menu. The Library folder will be shown and you can open the Library folder from there.) I drilled down until I found the V3/maildata folder. I quit the mail app leaving the one email account configured. Since, I am super cautious (30+ year computer programmer makes you that way), I copied all the files in that folder into a "safekeeping" folder and then sent the original files to the trash. When I opened up the Mail app, the app upgraded the mail account. I then held my breath (not required, but I couldn't help myself) and watched as the mail app downloaded mail and stop after downloading only really new mail. I was able to send email with no problems.
I chose to add his second email account in two steps. I quit the mail app. Then, I went to System Preferences -> Internet Accounts and added the second mail account through that interface. (It really would be helpful if Apple would let me enter all of the mail settings via that panel interface, but at least I could set the IMAP PATH prefix before opening the Mail app. I opened the Mail app. and took the new account offline (Mailbox -> Online Status and then selected the new account offline. Its mail had already started to download, but that stopped it) Then through the Mail Preferences panel, I fixed all the settings, i.e., unchecked the "Automatically detect and maintain account settings" box in both places, and specified the correct SSL port numbers for incoming and outgoing mail. I forced a save of the settings by clicking on the "Junk Mail" tab and responding to the pop up to save my changes. (A trick I discovered to confirm that my changes were saved) I then closed the Accounts panel and brought the email account back online. So far so good. The mail finished its download and stopped. Since the server certificate was already trusted with the first email account, I was not prompted to trust it again when I sent an email with this email account. The real test is when my husband goes out of town and tries to connect to his email via a different network. Fingers Crossed!!