Hi @thomascharbit — thanks for trying out Indigo!
Both approaches you described will work fine. You can certainly create one stack per site, or equally, put them all into one stack if they share similar infrastructure. I personally have complicated infrastructure but few sites, so I have a lot in one stack. It's nice being able to turn that all on with one click too.
However if you have many different sites which don't really relate to each other, and you'd prefer to work on them one-at-a-time, a single stack per site makes sense.
I've wondered whether it would help to have a quick explanation somewhere in the process of the app's first launch about this? I'm not entirely sure where it would go though. Any thoughts?