Multisite with sub-domain and sub-directory

I have so far running my multisite system with sub-domain structure.

Now that I also would like to add a few sub-directories to the main domain.

Can this be done on a single multisite installation? I have created new subsites changed the domain names to /case1, /case2 (like above example), but I only end up with 404. Could be mis-configuration on Nginx conf, but no clue so far.

If I have to have a separate multisite installation, (which in fact is a preferred option for business purpose), I wonder how I should settle configuration issues.