Firmware 2.01 should be able to access the second SD card. To access it you need to mount it, either explicitly by sending M21 P1 or implicitly by changing to the second SD card in the DWC or PanelDue file list page.
Bad colours on a 7 inch non-integrated PanelDue usually mean that the firmware for a 5" screen or an integrated 7 inch screen has been installed. Recent versions of PanelDue firmware have red, green and blue colour gradients on the Setup page, to help you check that the colours are correct.