This is how I got it to work for my R290s.
Make sure to remove all traces of prior drivers before going ahead, if theres left over remnants of catalyst or intel it will cause a crash. Get some driver removal apps, boot into windows safe mode and clear them both out.
1. First, I set the onboard as primary, then I go and install the intel drivers, reboot into windows again to make sure it works.
2. Reboot, go to bios, set PCI graphisc as primary, plug hdmi cable into the top R290, boot into windows, install the latest catalyst drivers. Go to overdrive, disable crossfire, set a desired fan speed or temp target.
3. Reboot, go to bios, set onboard as primary, boot into windows with HDMI cable in a R290 (I have VGA cable for onboard and HDMI for R290), once in windows (you will have no signal until windows is fully loaded), put the VGA plug into the onboard, pull out HDMI plug, monitor will black and reset for a few seconds then it picks up signal from the onboard and works fine. There's no monitoring of temps even when it works, but the fan ramps up as normal, overdrive is still in effect.
Thats how I use the PC while both R290s are mining maxed out. If I want to game, turn off the main card mining, pull out VGA cable, plug in HDMI into the main R290 and catalyst comes back into effect with proper monitoring and games will play just fine, with the 2nd R290 still mining full blast.
Edit: If i need to reboot the system or a clean start, i use the HDMI cable in a R290 to boot into windows, before switching it to the onboard VGA. You need to boot in windows with the R290 active so catalyst can apply overdrive settings properly.