Firstly, I must declare an interest. I have been asked to post this problem by the owner of my local and have been promised a bottle of something (should have clarified what) if this problem is solved.

The problem is the remote should open the roof...remotely...but tends not to, however it does go through part of the opening process if he moves to the passenger inside of the vehicle. Roof opens fine from inside car.

Do not know if connected to problem, but the boot flooded with water about three months ago. It is now dried out. Additionally he has bought and fitted two new Mercedes batteries.

Any help appreciated. Am thirsty!

Simple (maybe). I believe - and may be wrong - that the key operates on two systems. For locking, it uses radio, which works on a pretty long range.
However for doing the roof, it uses infra red, like a Tv remote, and you must point it in the right direction just like a tv remote. The sensor is in the door handle. If its only working on the passenger side, probably the sensor on the driver side is broken?

Am I right? Do I get a drink too?

What year is your Sl ? As to my knowledege this was never an option on the earlier models. As mentioned if your car does have this option then it sounds like the drivers door handle is faulty as you have to be roughly within 1 metre of the door aiming the remote directly at the black square on the handle & then pressing firmly & holding the lock or unlock button until the roof is fully opened or closed.
From what you have described though it sounds like your car is not equipped with the remote roof open/close feature & it just has the standard convience open/close feature that just locks & closes the windows or unlocks & opens the windows.

My early SL has this feature but I got bored of waiting for it to open so don't know if it goes more than half way!