I grow in a living super soil outdoors in fabric and yes, you can lose nutrients from excess watering. If your runoff is dark with tannins then you are losing some nutrient value. The soil I grew this year was a bit too hot for my seedlings and they were languishing in it so I flushed their solo cups with a molasses and powdered seaweed tea. The seedlings perked up nicely after that. Young plants in my experience are not fond of an overly rich medium and do better in a more benign soil. When the plants become more mature you can pump up the nutrient content with a simple top dressing of fresh super soil. It's good practice to fully water the entire container so that you maintain a good microbial balance throughout. Layering your soil is a smart choice but I found that "pocketing" works better for me. By pocketing, I mean creating different zones within my container that contain varying nutrients my plants may need during its lifecycle so the roots can choose where they need various nutrients from without creating a stratum effect the roots must pass through. I add pieces of fish to certain pockets for nitrogen, potassium rich soils in other pockets, and phosphorus soil to others. Another tip is to try and let your final container develop for a couple weeks prior to transplant. Water it regularly just as if you were growing a plant in it. The microbial presence will work wonders creating a PH balance in your container.