You got it right.  The lower bolts and the top studs have a shoulder on them.  The idea is that outer washer and the nut bottom up on that shoulder so that there is a tiny bit of clearance left over so that the shock is free to move a little.

When the swing arm goes up and down the angle changes and the shock needs to be free to rotate a slight amount.  If it were absolutely tight it would resist the action of the suspension.

However, like anything you have taken apart, check the nuts before you ride just to make sure they haven't backed off.