The general idea is that you clone the development repo and set it up (done so far AFAIK).
There are 2 folders intended for putting your app data. First, there is a global folder apps_extra in data. This is shared across all instances. Second, you have a folder within the corresponding server instance (e.g. inside workspace/server). Which one you chose depends on your app (does it support all NC versions or just one?).
You typically checkout the app directly in the corresponding folder. There you set up stuff and work as expected. You can add multiple worktrees if you need to use different branches for different app versions.