Answer: Certainly it is not a good idea to leave seedling pots sitting with their bottoms submerged in water. This would cause the soil to become overly wet and soggy. With capillary matting however, the bottoms of the pots are on the mat, not submerged, and the water uptake is more controlled or limited. At least one end of the mat however needs to be soaking in water so it can wick it up. You will want to set the mat on a waterproof surface because it is damp. When using the mat, you would not be watering from the top after the initial watering to settle the transplants. Make sure you are using a well aerated, free draining soilless mix, too. You may want to experiment ahead of time with some soil-filled but unplanted pots to make sure your set-up works as expected.
If you are just looking for a way to keep seeds damp until they germinate, it is simple to use a barely damp soilless mix, plant the seeds, water lightly to settle the soil, then cover the pot with plastic wrap or a piece of glass. Leave that in place to maintain the humidity level until the seeds germinate. Once they sprout, remove the lid immediately.
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