Overnight stopover with Air China- does it count as a 'visit'?

Australian citizens: We have a double entry visa for our 2 stops in Beijing in February but we also have a 12 hour overnight stopover at hotel provided by Air China in Beijing in January- I have been told this will be visa free entry but will customs stamp my 2-entry visa and therefore mean I can only visit once more? or will my double entry start after this visa free entry?
In the event that customs do stamp my double entry visa for this short stopover, could I then apply for another single entry in Tokyo?