I do exactly this - use the IGP and a discrete Graphics card for two monitors no problem!
I have:
Gigybyte H87-D3H motherboard
i5 4570 with HD 4600 IGP
HD 7850 Discrete graphics card
1 Asus 27" monitor with 1920x1080 resolution --> hooked up to HD 7850 graphics card via displayport cabel
1 Dell 22" monitor with 1680x1050 resolution --> hooked up to the i5 IGP via the motherboard DVI connection and cabel
Windows 7
This setup works no problem whatsoever - all plug & play and I move around all kinds of windows and applications. I play large games on the 27" monitor with the graphics card no problem and at the same time have browser windows running on the 22" monitor.
In adddition entire setup confirmed with CPU-Z and GPU-Z. When I start GPU-Z it shows in the dropdown menu which GPU should be shown. I start up GPU-Z two times showing the stats of each GPU correspondingy
So I cannot confirm all these "difficulties" with using two GPU's in this fashion - it all works fine