when used as VERB, it means
-the location when attached with -에 to present
eg. 지금 집에 있다. I am at home now.
-the state somebody being there
eg. 가만히 있어라! Just stay there!
when used as ADJECTIVE, it means
-the presence/existence/possession of something
eg. 이 세상에 귀신이 있다고 믿는다. I believe ghosts do exist.
TO answer your anther question
it should be attached with -느냐고 or simply abbreviated as -냐고 to do the reported speech for question
eg. 지근 집에 있냐고 했다.