We see too often pictures of wargames, particularly from the Second World War, of infantry bases perched on top of buildings to show that they are actually inside the structure.
Here is my alternative suggestion (used in 6mm/1:300/1:285) for these situations where building models tend to be solid.: For each building, take a small playing card of the type found in Christmas crackers or available very cheaply from Amazon. (For larger scales a normal playing card could be used to accommodate the base(s).
Slice off one side, showing the value and suit. This is your marker, to be slid under the building, folded such that the card value is displayed.
Place the occupying troops on the remains of the card, off board, for identification.
I find that this method gives a minimal display of tokens on the battlefield, while allowing easy recognition of who is occupying solid building models. I hope fellow gamers will find it useful.
Just as an aside, this method can be used to show you which buildings are occupied, and by what, without your opponent knowing from his side of the table. Perfect for ambush situations with no argument.
General Whiskers' semi-historical wanderings 