With new motherboards you can leave it on if you want to. If you turn on multi monitor support on in the bios and set the new gpu as first video device you can run more then on monitor at the same time. If not in the bios turn off onboard video.
Go to Bios by pressing "Delete" key when you turn on your PC, in Bios settings go to Advanced Bios Features> Init Display First> select PEG and thats it