You've got it all wrong......
"The reason i want to plug it into my motherboard is that i'm getting a new monitor in a couple of days and my motherboard has dual dvi input and my GPU doesn't. I am using an Inno3D Geforce 560 "
When you get your new monitor , just plug the DVI Cable that comes along with into the second DVI Port on the GPU. Leave the IGP as is, you don't need to mess with that at all. Forget you have a mobo that has a VGA port on it.
IMO, you're trying to match up things after reading the specifications of the new monitor and that says, you need a Dual DVI Link...... Don't worry here's a little something more for you to read. Laater down in the reply.
Your GPU
Connect each one of those ports to one monitor each.
"The Digital formats are available in DVI-D Single-Link and Dual-Link as well as DVI-I Single-Link and Dual-Link format connectors. These DVI cables send information using a digital information format called TMDS (transition minimized differential signaling). Single link cables use one TMDS 165Mhz transmitter, while dual links use two. The dual link DVI pins effectively double the power of transmission and provide an increase of speed and signal quality; i.e. a DVI single link 60-Hz LCD can display a resolution of 1920 x 1200, while a DVI dual link can display a resolution of 2560 x 1600. "