atitool needs the bios to find the default clock speeds of the card (they are only stored in the video bios). the problem when you have multiple cards installed is that only the primary vga bios can be accessible in the system.
so atitool guesses and assumes reference clock 27 mhz (which is correct for all ati video cards) and takes the current settings at the start of atitool as default frequencies.
this should not be any problem for you. atitool will work fine - i have been using atitool in a 2 (sometimes 3) video card configuration for over a year, so i would say enough tests have been done