Since the 'disks' [actually squares] are presumably somewhat permeable, soak up and allow some water to pass/diffuse through, I would presume the 'disks' would work positioned either up or down. The 'disk' material saturated with copper ions should keep the roots away no matter the orientation.
Part of the conflicting instructions could be due to different bottom 'disk' systems formerly or maybe still being sold in Europe vs. U.S., with U.S. just using a single sheet, while I recall the EU version used/uses 2 layers/pieces.