It can definitely be a tricky combination, not just from a sonic point of view, but from an "ownership" or "reponsibility" point of view. I think the main thing is that you need both players to have good ears and respect for each others space, otherwise you'll have many clashes or the low-end will suffer.
I've had a number of jams with both fretless and fretted players and most of them have been great, but mostly because the guys are good listeners and know when to switch between soloing and holding down the bottom end. I think Stick and fretless works particularly well, as the sonic signatures are quite distinct, not to mention "typical" playing styles.
I'm also in another project, however, that is continually degenerating into low-end mud, mainly because the other guy doesn't have a very good ear and just plugs away without taking much notice of what I'm trying to do. Kinda like how I often wail away on the melody side or launch into crazy melody arpeggios, ignoring what the poor guitarists are trying to do, hahahaha.
Cheers,
EG