The water level is dependent on high you have it and how strong your pumps are. ( I went to a single pump) but you don't want it too high normally the center section is lower then the other two. Water flows into the outside baskets, into the next two ( in the bottom) and then over the walls into the center section.
I didn't think of plugging those holes. I went to a sump inside of my stand. I plugged the left side overflow. In the left I have filter media ( in a intank basket - see my YouTube video about it ) top basket is filter floss then poly filter, middle basket is matrix and last is purigen. In the right inside basket I have my innovative marine bio pellet reactor. From there the water flows through the center section over to the left. I have a Tunze overflow 7004/2 that not only has a skimmer at the height of the water but also has a tube that goes to the bottom of the basket. The water then flows into the stand into skimmer through a refugium with more live rock and sand and then back up and out of the original nozzles.
But I might plug those holes as well is there two or three?
Here is a picture of my sump