I do both top and bottom water depending on the size of the plant and if I have time to baby each plant. After transplanting i do top water to settle the soil and get any air pockets out.
Maybe your problem is starting seeds in the cup. I start all seeds in a community pot/tub/6 paks then transplant after the first true leaves develop into the cups so I can bury the plants deep and it's usually in the lower 1/3 of the cup so bottom watering will work.
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