Can I cover the mat? Will the FIR rays and ions go through?

Of course, you can cover it. FIR rays, ions, and N.P. a charge will penetrate through the covers, pads, towels, or sheets.

You can start with as many layers as you need to feel comfortable.

There are usually 2 covers (thick and thin) in the set, and you can add more if you feel that the mat is still too hard.

Of course, some heat will dissipate if the layer is too thick, but you can adjust the heating to a higher level to compensate for the loss. 

As soon as your body gets used to the mat, you may remove extra layers one by one.

You must cover the mat completely while preheating it.

If you cover the mat partially, the temperature sensors positioned in the different layers of the mat around all the surface will report different and controversial measurements to the main controller.

Finally, the controller may lose calibration and start to work incorrectly or malfunction.

So, please, always cover the mat completely while it is preheating to set level.