No, the reason solar covers work is because they prevent heat loss caused from evaporation. Covers are not really great at capturing heat from the sun, although they help. What they are good at is keeping the heat in, especially at night. The only way they can do this is as a vapor barrier, so best to lay the cover directly on the water.
I have read that 75% of a pools heat is lost through the surface from evaporation, so if you prevent the evap, you save the $.
Just order a huge cover and cut to size, or use 2. The better the coverage, the more efficient the setup will be.
With all that said, I don't use my cover, and "Eloser" up top said he doesn't use one. From what I've read, it would save us a good chunk of heat though...