From my experience, you would start with your new Macbook, and then transfer all non-Apple files, folders, etc. from the old Mac to the new one. Don't quite understand what you mean by "the old one does not recognize the newer one". Migration Assistant would be launched from the new Macbook. By the way, how are your two Macbooks connected?
Recently, I did something similar, in that via a bootable SuperDuper! backup, I 1) erased and partitioned the internal SSD on my Mac MIni, 2) installed a fresh version of Yosemite (OS 10.10), and 3) used Migration Assistant to transfer all non-Apple files, folders, etc. from that most recent SuperDuper! backup I had made of my Mac Mini on an external device to the internal SSD on the mini. It worked like a charm. (I then booted up the Mac Mini, and applied the OS 10.10.4 Combo Updater to get to the latest version of Yosemite).