I've read way too many stories on this forum about flooded E60s and the resultant fried control modules. So my question is what is the proper procedure to avoid this?

The information can be broken down as follows:

1. What are the potential entry points for water? (Under passenger footwell, Trunk seals etc.)

2. What parts fail and causes the leak

3. How to check for these failures

4. How to periodically clear drain channels.

Its been raining here in sunny California and I've noticed a water stain on the headliner above the right-rear passenger's seat (near the rear side airbag). What could cause this?

 

More than likely that is due to clogged sun roof drainage line.