The license merge is something you might have to discuss with your account manager.
Now merging both environment it might take a process, and it depends if the small company you are merging will keep using their domain, since the document rights might be complicated to apply in that case.
On that case, it would be worth it to invest on expert services for this kind scenario.
Another thought, would be adding the server on your corrupt management console and control both environment on one management console.
Giuseppe Novello Principal Technical Support Engineer @ Qlik