When you are using 2 GPU's each card has to have a copy of the information the other GPU has in order to know what the other is doing.
Be that 2 actual cards or 2 chips on on card.
So that means that if you have 2X 1GB of memory, that would be 1GB for each chip total of 2 GB for the card/cards.
Now say a game sends 512mb of info to the card, each 1GB memory allocation will receive a copy so now you have 1GB left of free memory and not 1.5 GB.
Not sure if that makes sense to you or not ?