Gmail emails sending out of wrong account without my knowledge in Mail app

Question

I'm having problems with my Mail app sending out emails out of the wrong Gmail account. This was happening to me in Mountain Lion amongst other Mail app headaches, and I was able to fix it after weeks and weeks of troubleshooting. In Mavericks, the Mail app was mostly working correctly.
When I updated to Yosemite (did a clean install), I thought my Mail app was working correctly. At the end of November, I had some iCloud issues asking for passwords for all my apps. I had to remove iCloud in System Preferences and I added it back on. Anyway, here is my issue:
1. I have three gmail accounts, let's called them: primary@gmail, subscription@gmail and business@gmail. Over a year ago, I removed the business@gmail from the Mail app because the job was done. The primary@gmail and subscription@gmail were the only active gmail accounts I had in my Mail app.
2. The beginning of December, I sent some emails out of [email protected] and the emails were in my Sent folder in the Mail app so I knew they were sent out. I didn't receive any responses to my emails and began to wonder. It wasn't until a friend emailed me on my personal@gmail and asked if I was using my business@gmail account again because he said I haven't responded to any of his emails he sent there.
3. I went into business@gmail in webmail and there were all the emails responses. I forwarded them to my primary@gmail account and in the Mail app I looked at View>Message>Raw Source and I saw that the emails first tried to use my SMTP from primary@gmail but ended up using my business@gmail account which was no longer active in the Mail app. So when the people hit "Reply" to my emails they were sent to business@gmail in webmail.
What bothers me a lot is that I was not notified by the Mail app that the business@gmail SMTP would be used and I deleted the business@gmail from the Mail app over year ago so I didn't even think of it. 
I went through my Mail Preferences Account Information and looked at Edit SMTP List. I had all these Gmail SMTPs there so I deleted all of them to start fresh. I left the iCloud SMTP info as it was.
When I tried to add a new Gmail account in System Preferences under Internet Accounts, it would only allow me to add one Gmail account and not another Gmail account. After a few tries, I was finally able to add the second Gmail account. I did go and look at Accounts in the Mail Preferences and I properly assigned the two Gmail accounts to only use the Gmail SMPT that is assigned to it.
Here are my questions.
Do I need to do anything else to make sure that the Gmail accounts in Mail app settings remain as they are and this doesn't happen again. I've made sure that business@gmail is not in my Previous Recipients or in my Contacts.
I've noticed that the SMTP for iCloud is listed as "None" some of the time and I have to keep selecting iCloud over and over again. I'm hesitate to remove iCloud from my Mail app because I had to do this at the end of November when I had the iCloud password thing happen and I had a big problem getting my Notes data back.
If I remove the Mail.plist in Users Library, would I have to go through all the settings in Gmail webmail and Mail App or would some of the settings be there? 
Any help would be appreciated.  

Answer 1

You set it up, and you failed to distinguish between the SMTP servers or assign the correct one to your copy of Mail (it doesn't actually know which is which, you need to inform it)
Open Mail>Preferences>Accounts (NOT Mail>Accounts) and go down to the SMTP server list, choose the correct server for each account then check the box that says 'Use Only This Server' for each account.
This is not automatic, you get to choose and if you don't then this will result.
Remove the non functional ones.