It depends how much you have! When my ds (now 22) was young, we tended to keep any buildings in their built up state in his playroom (were lucky he had a fair sized playroom). The rest (accessories, vehicles, figures) were stored in plastic storage boxes on his storage unit (think this was IVAR stuff from IKEA). The boxes would be arranged according to theme (e.g. construction/fire/police etc).
But you might have say a few police vehicles in a box with accessories and figures, which was fine, but all the small parts would fall down to the bottom of the box.
I still use ds's Playmobil (and have added to it) in making scenes. We are in a smaller house now, so don't have a lot of indoor storage. The boxes are now stored in my shed, but still arranged according to theme. But these days the buildings are disassembled, and the small accessories and figures are put in plastic bags.
So say, for hospital/medical theme I have a box with the main pieces of the hospital, plus the vehicles (ambulance, helicopter etc) then a plastic bag full of accessories (furniture etc) and a bag containing the figures. All in the same box.
I've attached a photo of the storage in my shed.