and you can turn it off by disabling session.use_only_cookies in php.ini
Actually, one should set session.use_trans_id to off instead.
oes a session still be passed on to the second window (opened from the first window that has already started a session), if use_only_cookies is enabled
Yes.
Basically, all that you're trying to do here is to maintain state, i.e. the same data is maintained over multiple webpages.
You can do so by using the query string (i.e. the session id appended to the URI), and also by using a cookie, if the web browser allows for it.