Fevitz don't get me wrong on this. The blend knob on the Bongo in the centre or towards the neck is just great for a nice focussed bassy sound - absolutely fabulous for ballads and the like where you want to fill out the sound. But it will sound very different from the Ray if you run it like that - great if it suits the music style, not so good if it doesn't.
When I got my Bongo (used via Duarte, who in turn got it from Stingray96161) the neck pick up was flat against the pick guard - BUT it still was loud!! I emailed CS and asked for settings as I knew the Bongo pick ups are hot - the settings they gave me were basically as per the HH Ray, with the neck pick up a hair lower. You will not lose volume by lowering the pu (well not a lot anyway) - in fact Golem talks about having them very low deliberately, to suit his playing.
I'm guessing you will have to lower the input gain and possibly the volume on the Bongo. I even used to have to do this swapping between a 2 band Ray and a 3 band Ray fretless - well actually it was a mid range issue with that changeover as the 3 band had more mid at centre detent and thus more apparent volume.
Or you could go with the type of thing Keko mentioned - I'm afraid I'm too lazy to have loads of extra outboard stuff.
TBone - not sure of the answer to your question - I think it only applies to PU wiring (not sure whether the Bongo is series or parallel) but the Bongo, to me, just has a plain blend knob which give you full bridge PU and one end of the range and full neck PU at the other, and a graduated scale in between - I have a further complication (nice one though) in a piezo, which also has a blend control - blend between magnetic and piezo.
On other MM basses you get coil selectors. And yes, you get more scooped sound with both pick ups running full (as with many two pick up bass) (this is very apparent on my SR4HH which has a fabulous scooped slap sound with both pick ups in H mode). I haven't noticed it so much with the Bongo though.