The water level in a toilet bowl is determined by the weir not the amount of water poured into the bowl, and there is nothing you can do to change it. Some water spots are larger than others, but that is determined by design. The tank on low flow toilets is not supposed to empty. The flapper is designed to close when the prescribed volume of water has emptied. The "extra" water in the tank provides a little more pressure for the water that is emptying. You feel on a particular flush that additional water would be helpful, you can empty it just by holding the handle are couple of seconds. It would sound like you defeated the low flow with the flapper you installed.