I don't think it is possible to have an underground portal because they cannot be raised or lowered to different heights or depths. However, there may be third party content on the DLS. For underground stuff, I think there is content called 'U-Bahn'.
...I just had a thought (rare for me, I know). You could dig a hole and put the portal in it. Then you could cover the hole with buildings and that. Try the 'Portal Basic Short' from the DLS to avoid creating too long a hole.
Best wishes,
Padster
