you need to run the pump when the cover is on to circulate the water otherwise just the top inch or two will only get warmer
leave the cover on at night, it will help keep the heat in
How about solar heaters? The panels can be mounted to a roof or set up on the ground, they connect to your filter system to circulate the water. I use to work for a swimming pool supply company they had several different products to heat your pool with. Here is their website if you want it www.poolsupplies.com
Do you put a ball under the poo cover? I heard it makes extra space between the cover and water and it makes warm air pockets. Is there anything I can do. I'm buying a solar cover. Do they work anymore than a regular cover