The way I use them is to represent instances of classes with cards as well. I sometimes will write the class of the instance on the card, usually just the first time I introduce it, then the rest will be blank. Off to the side I might assemble a little class hierarchy so everyone can see it, usually not. I like to use five colors of cards. One for each major object type in my system.
Related objects use the same color.
I then pick up cards and move them about as they communicate with each other. I stage a little drama where the cards are the actors and they move about talking to each other. An object which is composed of other objects will have those objects tucked under it slightly forming a little group. To represent objects passing objects I take a card and move it from on top of one object to on top of another. I represent a collection of objects by grabbing a little stack of cards and laying them on the table.