When you have an add in GPU it disables the onboard. you cannot run both. Why don't you run both monitors off the one card? or does it not have 2 inputs?
Please list some specifications (motherboard, CPU, RAM, PSU etc)
I've heard of some people using the onboard as well. Using 3 monitor set ups with on board cards in combination with dedicated ones. Unfortunately I have absolutely no idea how you would go about this. It may involve activating the onboard video from your bios, but then that may very well disable the dedicated card in the process.