Hi,
My Apple ID has not changed from the dial-up email address I created it with.
However it has been linked to an iCloud ID account.
I then got an @me.com ID and later an @iCloud.com one as well.
I can use all three to login to the web browser version of iCloud and see the same Mail, Contacts and so one info.
I do use the "Original" Apple ID and the iMessages Account ID and the @me.com in Contacts and on the iPhone as the Apple/iCloud ID for syncing the Contacts list.
iMessages sees the three IDs as Separate ID as far as the iMessages Server is concerned.
I have tried to "Swap" the @me.com ID for the older Apple ID but have been unsuccessful.
The two IDs you have should both work in iMessages (although iPhone and Mac should be using the same one)
The System Preferences > iCloud option on the Mac should use one or the other - that should then be the ID used in the Settings > Mail, Contact and Calendars.
8:31 pm Thursday; July 21, 2016
iMac 2.5Ghz i5 2011 (El Capitan)
G4/1GhzDual MDD (Leopard 10.5.8)
MacBookPro 2Gb (Snow Leopard 10.6.8)
Mac OS X (10.6.8),
iPhone and an iPad (2)