If this is the case, would it have worked if I had set the pressure plate to 0-6 instead?
Yes, although your pressure plate needs to be on the highest z-level you want the water. Putting it on the bottom of the cistern will close the intake as soon as the first z-level is filled, which will leave your two-level cistern half-full.
I read the instructions on the wiki for using a pressure plate on the bottom of a cistern to control it's depth, but they didn't make sense to me so I didn't follow them.
Pressure plates send an 'On' signal when the water level in their square is between a predefined minimum and maximum, and an 'Off' signal when it isn't. The state in which doors, floodgates, bridges, etc. are built is the 'Off' state.
So, to use the wiki's example, a pressure plate set to 0-5 and connected to a floodgate will tell the floodgate to be 'On' at a water level of 5 or less and 'Off' at a water level of 6 or more. Floodgates are built in the closed position, which means it'll be open when the water on the plate is at 0-5 and closed when the water level is 6-7.