Hi PMPosse,
If you have created Package using AAMEE 3.1 then you should not face this issue at all but if you continue to, then use the Adobe Provisioning Toolkit to Serialize the Products of create a Serialization file using AAMEE 3.1 and then execute it. It should fix the issue with Licensing.
For more details please refer to this Link and view the Adobe Application Manager, Enterprise Edition 3.1 (Mac) guide.
http://www.adobe.com/devnet/creativesuite/enterprisedeployment.html
Hope it helps
Regards,
Abhijit