Bart
Have AutoCom system as well... and have found the best place is under the pillion seat, if you re-jig a few tools in the toolbox, it fits in nicely. I cut a slot out of the side of the toolbox and all the wires lead in and out. Un-do the tank positioning nuts, run the leads under same and out near the dash (mind you don't pinch anything when replacing tank)... works like a dream.
Obviously you can't hook up the electrics to the rear light like other bikes (ABS won't allow this)... so you've to break into the wiring. Contact AutoCom technical advice... they've been asked this question by hundreds of BMW owners and have a detailed FAQ sheet prep'd. I e-mailed them, and had an answer back in less then an hour.
The other option is use the disposable battery add-on. You do incur some costs, but you can also remove the controller box in a few minutes if necessary. I use mine quite a lot, and haven't found the batteries disappear very quickly. Put it this way, the CD / Mini-disk / radio you plug into it will require much more battery changes than the AutoCom system.
Best of luck with it... makes riding a pleasure, not shouting back and forth to your pillion.. and music? Takes the edge of those long rides.