Do you rest directly on the mat or use the cover or simply cover it with a sheet? I have read that if you want benefits from FIR you need the red lights directly against your skin?

LEDs emit 660nm monochromic visible red light. It is not FIR. It would be best if you had the red lights directly against your skin. Only Purple Ereada® mats have this Photon function together with FIR. All other mats (Rich Brown, Gemstone) emit only FIR rays. 

If you use the mat for Far Infrared, Negative Ion, and PEMF, you may use the thin cover or thick padded protector with a 3-D Air Mesh Layer; both included in the set cushion your mat. 

You may also add some towels or sheets on top to make it more comfortable; when your body gets used to crystals pressure, you may remove all layers one by one.

But if you would like to use the Purple Ereada® mat for Red Lights, better to use it without covers.