As long as a drain hole is located at the lowest point at the pan water will drain out. No physicist could argue other wise. The reason your pan is holding water is because the hole(s) allowing water to come in are higher than the lowest point. I also believe that you are accumulating water on the inside while driving, not stopped. If you are accumulating water when stopped you need to look up to fix the problem. DannyP had a good idea when he said attach a short piece of hose to keep water from coming in.
Spydermike was correct that a drain hole will not keep water out and you will still get squishy carpet. A drain will keep you from getting standing water.
If you really are set on sealing the existing holes spraying with a water hose from the outside seems like a difficult way to find holes. Last year when my boat sprung a leak I had it hauled out of the water, removed the carpet and upholstery, made sure that any exposed electrical connections were sealed and then filled it up from the inside. Then you look for the drips. It's not a fast or easy thing to do. But you will find ANY place that is permeable to water. Remember, water can travel considerable distances along a seam before showing it's self on the interior. Don't be surprised if you find a leak on the opposite side of the car.