If the part before the @ in your @mac.com and @me.com email addresses are the same - then they are the very same email account, and all emails sent to either address end up in the same InBox.
Whether outgoing emails are sent from <yourname>@me.com or <yourname>@mac.com has always been your choice, and is defined in your email application settings by you. Apple have not screwed you up at all. It's entirely in your hands which of the two email addresses you use.
You could've kept using your @mac.com address if you chose to. Your @me.com address was added as an optional extra. Soon, you will also get <yourname>@icloud.com as another optional email address which will also recieve all email address to <yourname>@me.com or @mac.com or @icloud.com
Without more information about how you have configured your email account to store old emails etc it's difficult to advise what you need to do. In theory, if you have archived old emails offline, then all you need to do is move them back to the online mailboxes. Then all your emails will be together and searchable online.
Julian, thanks for the reply. I understand about the two being the same. My big problem is that when I search on my iphone for old emails, only the .me.com ones show up. If a client sent it to .mac 7 months ago, it will not appear. Sometimes I need to go back and check something or retrieve information. Also, my .me will not forward. I appreciate your help.