I know it mattered back when I had a Pioneer 6800, if I didn't hook up the AUX piece before the XM I would hear XM over anything coming over the AUX unit.

I plan to have XM (NavTraffic), Bluetooth module and the iPod cable. Wondering in what order they should be hooked up... or is the newer ip bus more intelligent?

Also I have not purchesed the Bluetooth module yet, I plan to add it shortly, so if I wait on that I want to be able to easily access and hookup that module in whatever place it should go into- knowing where it should go in line helps a lot

This might all be a moot point if the IP-BUS setup has gotten more intelligent then when I hooked up my FM903XM and Pioneer IP-BUS Aux Adaptor

The ipod cable plugs in to a different port on the D3. As for the bluetooth and XM, I think it really shouldn't matter as far as functionality goes. If I were you, I would hook the XM to the D3, and the bluetooth to the XM unit. That way the XM signal has less possibility of signal degradation as the path to the D3 is shorter (in theory, but it probably doesn't matter much). But if it doesn't work that way, it's easy enough to switch the cables between the two. I would dry fit everything sitting on your front seat, and if everything checks out fine, then install the modules and route your wires properly.