Journal Theme can be customised completely different in a multistore environment - assuming you have already created a multistore environment in Opencart. For more info on how multistore works in Opencart please see Multistore Documentation.
To use different skins, create a new skin in Journal > Skins (or duplicate an existing one) and then go to Journal > System > Settings and apply that skin to the store.
To use different menus, a different skin must be applied to the store (as explained above) and then headers must be also duplicated because menus are added to headers and headers are added to skin. So duplicate a header module in Journal > Header > You Header and then assign it as the active header in Journal > Skins > Edit > Header which you than assign as the active skin in the other store.
Since modules are added to layouts, you must configure different layouts for your stores in order to display different modules on a page, based on current store. Then simply duplicate or create new modules and assign them to those layouts.
The regular license only covers a single end-product, which in this case means a single store or domain. Multiple stores require one regular license for each end-product, regardless if the stores are created in the same admin panel via the Opencart multi-store mechanism or separate installations. Basically if the store is different in nature and uses a different domain it needs its own regular license.