JabRef “only” manages .bib files. So, your issue is more related to LaTeX and BibTeX than to JabRef.
The question marks indicates that, somehow, LaTeX does not find the references associated with your \cite commands.
To get your document with references, you need to compile with LaTeX, then with BibTeX, then with LaTeX again.
BibTeX will output 2 files: One ending with .bbl, the other with .blg. The .blg file logs the errors found by BibTeX. Its content may help you find out what is going on. Also, LaTeX creates a .log file that main content hints.