You say you're using passive pickups and have a POD... you should have no problem getting great sounding cleans. Use the neck pickup. Keep it in humbucker mode for thicker sounds or split it for brighter/chimey sounds.
EMG single coils sound great for cleans by the way... the clean tone on Cynic's Traced in Air for example. The 89 or 707 in single coil mode would do that sound well. I've heard fairly good sounds with 85 and 707 in the neck too, as long as the volume is rolled down, but it's not as nice as the single coil sounds. The 808 on the RG2228 8 string I had actually sounds really good for cleans too... it's lower output than the 707, and that guitar has a longer baritone scale so it's naturally brighter... the result is a nice crisp humbucker clean tone. If using EMGs, single coils are the way to go usually though, in my opinion...