How many hosts you have, in the vCenter Server, is dictated by which vCenter Server license you have... If you have the license that will allow the count of hosts you're looking to add, then you can simply add the hosts to the vCenter configuration, building the clusters as you need to.
You will want the vCenter Server version to be at least the same level as the highest level in any host... So, if you have a new setup using ESX/ESXi 4.1, you'll need to have vCenter 4.1 in place (make sure you read the docs for installing/configuring it, since it has changed since version 4.0)... You can pull the older hosts into the new configuration as you wish... Simply remove the host from the inventory of the old vCenter Server and then add it to the new one, in the correct cluster. You can keep the old vCenter Server kicking around while you do this, so that you have a "fall-back" position (CYA)...
I would make the vCenter Server as a VM... I've done this in the past couple of environments I've built (under releases 3.5 and 4.0) without any issue at all. Unless you have a LARGE host count, you can easily use a VM for the vCenter Server... You'll see even more benefits once you've upgraded from the base (Essentials) edition into something with more features (such as vMotion and HA)... The past two environments I've set up were using Enterprise and Enterprise Plus editions... Really, really great feature sets there... In my eyes, and the people I reported to, money well spent... I do understand that you cannot always get the top end, but see about getting the budget allocated for next budget year, for when it's time to renew the licenses, to upgrade the version to something with more features...
VMware VCP4
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