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. You really need the red lights directly against your skin for red light bio-stimulation. Only Purple MediCrystal amethyst agate mats and Tan ThermoGem amethyst tourmaline jade mats have this Photon function together with FIR. All other mats emit only FIR rays or FIR Rays with PEMF. 

If you use the mat for far-infrared, negative ion, or PEMF therapy, you can use the thin cover, thick padded protector, or 3-D Air Mesh Layer included with your mat to cushion it. 

But again, if you would like to use the Photon MediCrystal mat for red light therapy, better to use it without covers.