Typically, most motherboard bios will disable the igpu if a dgpu is detected, so without some set-up on your part, those graphics outs on the MoBo io-panel might not even be functional.
You should use the outputs on the dgpu.
Essence: That's what I've BEEN doing. I just spent $180 on a two-stick kit of RAM spec'd at what I'd been running their 4-stick overclocked successors. I had come to the conclusion that a glitch I had (random resets once every 5-to-7 days), was related to the number and tweaks to my RAM. It's nice to have a potential 4-channel kit sitting in the locker as I plan my build and budget for this year, but it wasn't necessary.
I thought that maybe my problem arose from the single GTX 570 dGPU I'm using, or maybe the LUCID software for getting the iGPU functional in the mix, but my "diagnosis" of the RAM was based on good observations but totally wrong.
During all that time, I was also poking around in forums and web-sites to examine other ways to use the iGPU. Now it may turn out this week that the problem was actually my graphics driver software in the two-monitor dGPU hookup, the problem may not have surfaced if I'd only used the dGPU for one monitor. And -- one monitor is an Onkyo AVR pass-through to a 42" HDTV, resolution 1920x1080; the other is an older LCD monitor set to its maximum 1680x1050. The HDTV connection also carries NVidia on-board sound.
So even if that were all true, I might just as well have put one monitor on the iGPU and another on the dGPU. I had this from a thread in which one user swore by his problem-free, two-adapter/two-monitor setup.
And someone here also informed me that counting on either NVidia or Radeon for graphics plus surround-sound (HT + "system") was troublesome, noting that the INTEL HD graphics of any flavor -- 2000, 3000, 4000 -- would suffice for the HTPC function.
I'm going to find out more this week, after observing what a driver-update brought me in stability and problem-resolution. But I think I may just try out the Intel HD 3000 for my desktop monitor, and it may eventually let me use a third monitor on the dGPU so I have iGPU with sound for HDTV and "system," dGPU-DVI(1) with monitor for "desk" and DVI(2) for a gaming 1080p.
In other words, with your choice of processor the iGPU is something you "have" that you can't get rid of for preferring a dGPU. Might as well use the iGPU if you can and it satisfies either needs or wants.
Here's a footnote: The iGPU isn't disabled for using the dGPU, but it is limited to 64MB V-allocated RAM if it's set to "multi-monitor for LUCID" support. You have a choice to use the iGPU or the dGPU as primary boot-display-adapter in the BIOS -- at least with my rig. If you make the iGPU the primary and avoid LUCID enabling, the iGPU can get as much as 512 MB of RAM. For a 16GB configuration, that's not a lot and it leaves plenty for other applications.