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The water separator is built into the fuel filter element (it has a coalescence filter to increase the size of water droplets to a point that can be effectively stopped by a hydrophobic membrane) which is under the driver side seat, behind the plastic that has the two big holes (if you crawl under the car you'll see what I'm talking about).
Water will get filtered out and will not go past the filter. I'd actually be worried about using any additives that may cause the water to go passed the filter to the HPFP or the injectors.
Like Mr Huffman said the two don't mix which is good thing (because the filter can stop it effectively) and you don't want to add something that mixes the two.
If the filter gets too much water and clogs you'll get a code, but I believe that it may not trigger the CEL.
You may want to think about changing the fuel filter.
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Last edited by ZetaTre; 10-30-2015 at 12:59 PM.
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