Can I purchase 4 VMWare Essential Kits and install four separate instances of VCenter? Am I allowed to use multiple VMware Essentials Kits in one location?
Unless I'm missing something, you can have how many Essentials Kits you want per site/location, the limitation is that each vCenter from Essentials Kit can manage only 03 (three) hosts.
Is it possible to install a single instance of VCenter for all 12 ESXI 5.5 servers with these licenses or do I need to purchase a different set of licenses?
No, each Essentials Kit can manage only 03 (three) vSphere ESXi hosts. To manage more than 03 hosts you will need the vCenter Standard and vSphere ESXi Standard, Enterprise or Enterprise Plus.
Anyway, there is still another options if you don't want go to more advanced license, like vCenter Standard and vSphere ESXi Standard/Enterprise, see: How to License your VMware vSphere 5.5 for Retail and Branch Offices (ROBO) - VMware SMB Blog - VMware Blogs