Would make sense to me to let the Onkyo take care of that...
I'm not knowledgeable enough to stack different EQ settings across a process chain. Preference is to let the device that can handle EQ best, take care of the works (for me) - especially when passing audio over HDMI. Would ask are you primarily concerned with music, or films?
In which case... I'll say that rather than concerning oneself with a utility that runs in the background, most 'player' applications will EQ things better than a terrible Dolby, Realtek, or whatever background utility. Jriver worked really awesome with my PC to HK. Foobar is solid too. For films I use PowerDVD 12 passing PCM to the HK to be taken care of. I don't let my PC do any decoding.
Your call. Hope what I spat here is accurate. I'm no pro and I'm sure 12 other dudes on here can offer up better advice.
Regards,