The number of models it is possible to place inside a building will depend upon its size. If the model building has roofs and floors that can be removed, then the models can be placed physically inside, which simplifies matters considerably. However, most buildings do not offer this kind of facility, so players must decide before the game how many models the building can contain. Obviously, models that are too large to fit into the building cannot do so - a Dragon or Troll is simply too large to fit into a cottage!
Unless your buildings have removable roofs and floors you will need to keep a separate record of where models occupy a building. This can be done in any suitable manner, for example by writing down bow many models are inside on a scrap of paper and placing the piece of paper under or beside the building. Point out to your opponent where troops are moving into buildings to avoid any confusion later on.
Except where buildings are really huge, you will not need to move troops about inside. Models inside the building are assumed to be wherever you wish, and can shoot from any windows, doors or other openings as opportunity permits. However, if a building is very large, roughly speaking more than 6" along any side, then this can lead to unreasonable situations. If a building were 24" long for example, it would be ridiculous to allow a model to romp from one end to the other in a single turn. Should you wish to employ such grandiose buildings then you must be prepared to either make them in such a way that models can be placed inside, or record movement within them by means of graph paper charts or maps, noting down where models are each turn.