Hi @nadodi As you’ve found, there are installation conventions for the plugins you mention (I’ve not used BadgeOS, but it appears to work the same) that won’t allow you to configure a Commons in a Box install the way you want it.
CBOX considers each multisite install to be, in effect, a single community. What you seem to be after is perhaps better described as a “community as a service” situation – it sounds like you want each new site on the multisite install to be an autonomous community, though perhaps linked in some way to the main site.
You could implement this to an extent by considering BuddyPress groups to be your “communities” and using group blog for posts and pages that are independent of the main site. BadgeOS (via BadgeOS Community Add-on) will work with your BuddyPress groups, although you won’t have independent levels and so on.
You could also look into setting up a WordPress multi-network instance using either Networks for WordPress or WP Multi Network. You could create separate networks for each subdomain, where each network uses “subfolders” for its internal sites. Then, in combination with BP Multi Network, you can create multiple CBOX-enabled multisite instances using the same WordPress codebase. You have to remember, however, that there is still one user table shared between all the networks, so your segregation of community membership could be problematic.
My question to you, I suppose, is why you want this particular setup? Is it just the administrative convenience of a single codebase? It sounds to me like you’re actually after independent sites, where each subdomain is – in its own right – either a single WordPress instance or a multisite instance.