Slot doesn't matter.
If you are trying to flash a BIOS for a different card then you will get a security warning that the BIOS does not match your card. If you are absolutely sure that the BIOS is compatible you can use the -f parameter to force flashing. For example atiflash -f -p 0 BIOS.bin
Don't do that. Or specify the number of the card if you want to flash ASUS bios for example, and your card is from Sapphire. The article explains it well.