Question about starting treasure tokens

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Each faction pack comes with 6 treasure tokens (two 1's, two 2's, and two 3's).  

At the start of each game, you are supposed to shuffle treasure tokens and place them on the battlefield.  

Are you supposed to use all 6 tokens for the 3 spaces on a side of the battlefield?  This seems like it could lead to unbalanced games where one player has two 3's and a 2 while the other has two 1's and a 2.  

My friend and I have played a bunch of games and used a house rule that has us both start with 3 treasure tokens (one 1, one 2, and one 3), shuffle them up and place them on the board.

I will soon be playing a tournament and want to understand this rule correctly.  

Thanks in advance for your help. 
Just a quick clarification point - the tournament I will be in will be a faction pack tournament (play out of the box, not constucted).