Installed the MKI9200 in several E46's (same sound system); if you have nav and use a SOT lead it will overpower the BMW sound so you can't hear the nav. and since it has an interal amp it will never sound as good.
If you can, connect it via the AUX in on the head unit using the AUX install wires that come out the blue box. the instructions list that as an option, that way you can control the volume and tone using the BMW head unit and offers better sound.
The best place for the mic is routed round the A frame and place up where the wing mirror is, this limits interference from the electronics in the dash and will offer consistent pickup without your hands getting in the way or you moving out from direct line of sight from the mic.
There's no really good place for that annoying screen, there's also no option to reroute it to your nav screen either. from experience the least offensive place is to mount it to the right of your headunit, or near the right side fixed window demister.
The whole point is to position that screen so when you look at it you don't become a hazard on the road by being distracted or taking your eyes off the road too much, try to remember that.
The little remote secures very well just behind the wheel air bag sort of through the left(or right) quarter gap on the wheel, there's a flat space you can double sided tape it too. it's hidden but fully accessible without letting yous hands stray from the wheel. since it's attached to the wheel itself, you'll very quickly get used to it being there and will learn the button placement easily, also since it's on the inside you won't clip it during spirited driving.