Which way will water go?

It depends on the tension in the cover. If the cover is pulled tight, the water will tend to go from the top to the pool.

If the cover is loose, the water will tend to go from the pool to the top.
 
Water will tend to go from the pool to the top of the cover while the cover is loosely sitting on the water.

You can reduce the amount of water that goes through the cover by pulling it out some to increase tension, but don't try to make it sit above the water.

Think about it as if the cover was porous mesh. It will reach equilibrium and sag based on the tension.

Try to keep the cover clean and pumped off and snug enough to keep the wrinkles out but not tight.
 
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