Not sure what you mean by the different layers. Limewater itself is clear.
If you let it sit around but covered for a day or longer, it will settle out with solids/mud on the bottom, maybe a crust of calcium carbonate on the top of the water, and clear limewater in between. How long that takes may depend on the particle size of the starting calcium hydroxide, smaller particles settling more slowly.
If CO2 from the air can access it from the top, then you may continue to get calcium carbonate forming through it over time, and it may not become clear for a very long time.
In general, it is best to add the clear liquid. Milky limewater can contain very high and variable amounts of solid particles which can drive the pH super high if too much is added. The clear liquid also avoids some impurities that are likely to be in the mud on the bottom, including copper, phosphate etc.
This has more on what solids are what in limewater dosing:
What is that Precipitate in My Reef Aquarium?
http://reefkeeping.com/issues/2005-07/rhf/index.htm