To start - you can do one host at a time by putting it in maintenance mode first - then preparing it - then remove it from maint mode. Doing this should have no impact as the running systems in the cluster as they should be moved off to the other systems while the host is in maintenance mode.
That all said... cloud is really designed to be the only function running on a cluster - it CAN work in a shared setup but this is not the preferred way of running it. The standard setup would be to have a cluster without anything else that cloud can fully control. (If this is not possible you can create a resource pool on the cluster and let cloud control that)