If the cup filled overnight, there may be something in the water column causing exessive foaming (i.e. water conditioner, frag epoxy etc.). With the riser all the way down, the water should be VERY low in the skimmer neck. You can use an airtap to lower the air intake while the skimmer breaks in, and or the stuff in your water is removed
IMO, and the way I run my ER, I start the water level about 1.5-2" from the TOP of the riser tube.
Your skimmer may take some time to break in, and until then, it will be very difficult to set the water level in the skimmer. This is stadard.
HTH
Jim