I worked on my graphics card on the basis of what you told i.e "Some MB's disable the pcie slot when using Integrated". So I put connected my VGA cable to my ati card and rebooted, I could not see anything on the screen but I had selected CD Rom as my boot deivice.
Then when it booted up the CD, I saw DVD ROM light blinking then after all light got disappeared in DVD ROM and Hard disk, I typed the location atiflash utility blindly in the DOS and typed atiflash.exe -i. Then I switched my graphics cord to my IGP and then checked that the card was being detected..
I then plugged out that wire and flashed the BIOS accordingly.... !!!! NOW ITS WORKING LIKE CHARM
.... THANKS MAN !!!