Hi,
when you say "cell" I presume you mean resource pool.. vCloud has full control over all the resources it creates in the resource pool (and any sub-resource pool). Technically you could create stuff in there outside of vCloud but it would be a very bad idea as vCloud controls the resource pool settings (reservation / limits etc) and you would probably confuse it. If you want to share a cluster then create a Resource Pool just for vCloud and put your other VMs outside of it.
With regards to your second question, vCloud installs an agent on each host (known in vCloud as "preparing" a host). To install this you need the root credentials of the host. vCloud also communicates with vCenter.
Tim