Not necessarily, units are deployed to a “machine”. Machines can be containers, but they could also be the bare metal servers themselves. Where things get confusing is that it is also possible add further machines, that are containers, within your current machines (juju add-machine lxd or, less commonly, juju add-machine kvm).
Adding a remote LXD cluster as a cloud has an advantage that it has its own concept of availability zones. A potential disadvantage is that all applications will deployed to containers.
It sounds like what you probably want though is MAAS. That gives you access to your bare metal servers as machines if you need them, the ability to use LXD containers and more automation.
If you would like to use the manual though, that’s an option too. For each data center, run juju add-cloud, then juju add-machine ssh:<user>@<host> for each node.
Happy to provide more info if that would be useful. Sorry that there’s so much to cover before you get started.