Since no one has replied yet, I will. I don't have a Ray, but I play worship team with a Bongo HH and a Sterling HS. I'm not sure what pickup config you're talking about, but when I'm just using the bridge humbucker on the Sterling, I leave the EQ pretty flat, maybe boost the low end a little (like 5-10%). If I include the neck pickup, then I'll usually set the low flat and boost the mids about 10%. The single coil is kind of bright so sometimes I'll cut the treble by 25-50%. On the Bongo I usually have about 60/40 neck/bridge, and I'll boost both mids, treble flat, and decrease the low by 10% because that bass has so much output.
I'm running direct into a compressor and a SansAmp. And sometimes I'll throw in some overdrive (Darkglass B3K) to thicken it up. To put this in context, we've got a 3500 seat worship center and we do stuff like Hillsong, Phil Wickham, Chris Tomlin, Bethel, etc.