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The vSphere Essentials Kit is basically an acceleration kit. It includes licensing for 6 CPU sockets (dual socket CPU's are being assumed) and it includes a vCenter Server Essentials license (3 host maximum in the inventory). With vCenter Server you are able to manage all your 3 hosts in 1 inventory. You don't connect to each host individually but you connect to the centralised server, the vCenter Server.
After you've ordered the license, you will get an e-mail with your license keys. You can then go into the license manager (Configuration -> Licensed features) of your ESXi host and add the license to the host. Basically, the same steps you took for assigning a free license for the host, but now you do this with a paid license. The maintenance fee is required (and included) with the first year, after this, you can choose for yourself if you want to extend the support or not.
If you have shared storage between your host (either iSCSI, NFS or FC) I would advise you to look at the Essentials Plus kit. Essentials plus offers even more features as it provides stuff like vSphere HA and vMotion which is really, really cool stuff, but it requires shared storage. These more advanced features are also included with the standard license. The global idea behind the essentials kits are to provide the SMB branch with a relatively cheap way to host and license an ESXi server.
Hope this helps,
1+2.) You only have to enter the new license keys. No need to reinstall the hosts or shutdown the VMs. In oder to manager all 3 hosts from the same management interface, you have to setup vCenter Server, which is included in the Essentials Kit.
3.) After initial purchase, it's your decision whether you renew subscription after the first year.
4.) There have been a couple of changes in licensing since vSphere 5 was released. With the release of vSphere 5.5 all the hardware limitations (Cores-per-CPU and RAM) were removed (see http://www.vmware.com/files/pdf/vsphere_pricing.pdf).
5.) See page 6 in the Licensing, Pricing and Packaging White Paper
Thank you very much, your answers are very clearly!