I have spent weeks hunting for these little drain exits and after spending Saturday morning taking the front arch liners off and only finding spiders and mud i finally found them under the car, towards the front by the jacking point.
Basically you need a Jack, Axel stand, torx set and an 8mm socket.
Jack up the car and starting at the front remove 5 of the hex screws on the sill cover from underneath. Then using the 8mm socket remove all the bolts holding the undertray to the body from the back to the front. you need to remove them all as you want to drop enough down so you can flex this cover away from the other plastic mouldings.
Once the bolts are removed, pull the underbody cover down and feel on the inside of the sill from underneath. The drain exit is between the jack and the front of the sill.
To unblock, get your preferred twine or washing line and start poking. mine took a meter or so before a great whoosh of water came out.
I had exhaused all possibilities to unblock my drains (compressed air, twine, washing line etc). and NOWHERE could i find a picture or description of where these were on the e90/91.
I really hope this helps others looking to sort our their leaking sunroof and blocked drains. I now have very intimate knowledge of how to remove headliners and most of the wheel arch and underbody trims
