You can pour your mixture right into the top of the glass at the opening. Make sure that the stopcock (the plastic valve at the bottom) is in the closed position, so no liquid will drain out from the bottom until you are ready. Once the two liquids have settled, you can drain the bottom component using the stopcock.
You can also shake the funnel (while fully sealed, of course) to agitate the mixture, or simply invert it multiple times. Of course be careful not to shake too vigorously, as emulsions can result. In the case of excess vapor pressure, make sure you can properly vent the top.