When you create an encounter you can put tokens on maps, placing them wherever you want. When you run that encounter they appear on the map in the right place.
But if i'm not mistaking the size and orientation of the tokens are not saved.
please vote here http://fgapp.idea.informer.com/proj/?ia=141836 to have pre-positioned, pre-sized and pre-oriented tokens in your encounters if it is at all possible with Unity.
thanks