It's actually the bottom reservoir you must fill; it is connected to the primary, or "active" tank, from which the DEF injection system gets its working supply.
The top filler is for the secondary (passive) tank, which you can try and fill (but it's a bit messier since the tank is above the level of the filler tube, you will always get some DEF burping back at you when you fill the passive tank, no two ways about it).
As an aside, most larger DEF jugs (2 gal) are starting to come with the narrow insertion nozzle that will fit into the fillers.
2009 335d Sport - Space Grey
, Gloss Black
on Black Leather