Yea, I know what you mean.
OK there is a couple things you can do. First take a look at your overflow. See if a short length of the black 1/2 hose fits into the top and is snug.
If so, its like mine and you can cut the fitting down so the water doesnt go so high.
Then later when you want the water higher just put a piece of tubing in there to raise the water level.
The second thing is you can raise the cube. get small pots with holes on the bottom and put a small amount of hydroton in there, set the cube on that. This is how I did it and it seems to work.
This cube is probaly larger then what you are using but see how just the bottom is wet? It also helps when transplanting
Third is you can get a didital timer and run it for as little as one minute. That may help you.
Best thing to do is to remove the plants and get some dry rockwool in there and test different things. You can do it.