I've not read anything on whether or not Nicholson knew Polanski was at his house. However, Huston was there. Here is a link to scans of the girl's original grand jury testimony; http://www.thesmokinggun.com/archive/polanskicover1.html
The girl says Huston told her she had to go to work, but it seems as though she's still there. She knocks on the bedroom door afterward and talks to the girl again after she got her clothes back on (she'd spoken to her when they first arrived).