All I can say is this, I mixed guitar and chiptune once, put about fifteen minutes total into the production of the track, and a bunch of people shit their pants with joy. Ok, not really, but it seemed a lot of people liked it. Listen: http://wizwars.good-evil.net/MP3/ccn016
y_Away.mp3
Aside from writing the actual chiptune, that song took about ten minutes to record and like I said, maybe fifteen minutes to play around with the EQ and volume of the chip and guitar. The guitar tracks (two tracks hard panned) were recorded clean and then processed with some basic 'metal distortion' setting in Amplitube 2. It should also be noted that I recorded it using a very shitty Squier guitar, I think one of the lowest models you can get actually.
The reason I bring all this up (aside from shameless self promotion) is because sometimes it's a good idea not to over think things. Just play with the EQ and volume until you find the sound that is desirable to you, then take note of those settings and use them in future recordings as a reference point. I don't think there is really a right or wrong way to do stuff like this.