Hello,
You are receiving this Over Deployment Message as SEPM 12.1 bases its license count on the total number of managed clients , regardless of whether they are 12.1 or 11.0.x.
Check this Article:
http://www.symantec.com/docs/TECH178829
You could not Merge 2 License in 1. However, I would suggest you to upgrade your SEP11 license to SEP12 online
Check the Article:
How to upgrade your SEP11 license to SEP12 online
Once the Upgrade of License is done, you can download the Latest SEP 12.1 License and Install the same on SEPM which would now carry 2 Licenses [Old SEP 12.1 (2500) and New SEP 12.1 (1500)] making them to 4000 Licenses.
You can Later Activate your License from SEPM. Check this:
http://www.symantec.com/docs/TECH162623
Also, check this VIDEO :
Licensing Guide for SEP 12.1-Part 1
Licensing Guide for SEP 12.1- Part 2
Hope that helps!!