Hi,
If you had one iPhone and linked to to your Apple ID and then get a second iPhone with a different Number and then add the Apple ID to that iPhone that Mac version of Messages (and any other iOS device) should list both iPhone Numbers.
To remove it from the Receive At list (and therefore the Send From as well) do this:-
Open a Finder window.
Use the Go Menu whilst holding down the ALT (Option) key
Select the Library that appears and navigate to the Preferences folder.
In here find com.apple.ids.service.com.apple.madrid.plist
You can Drag it to the Trash and Restart Messages.
You may need to re-add you Apple ID.
A further restart of the app should get the Pop ups about the current iPhone (if you shut done Messages for the old iPhone)
IF you have Xcode you can edit the .plist by double clicking and then deleting the unwanted iPhone number.
7:46 pm Thursday; April 24, 2014
iMac 2.5Ghz i5 2011 (Mavericks 10.9)
G4/1GhzDual MDD (Leopard 10.5.8)
MacBookPro 2Gb (Snow Leopard 10.6.8)
Mac OS X (10.6.8),
Couple of iPhones and an iPad