I find it best, when using two puppets, to have the puppeteer on his left to have the puppet on his left hand and the puppeteer on the right to have his puppet on his right hand. (Left on left and right on right.)  If you have a left hander, this works even better.  They will both be able to put their puppets closer to the stage this way and puppets will be able to face each other more easily.
If you are using three puppets, then the one in the center puppeteer should have the puppet on the right hand if he is mostly talking to the puppet on his left.  Remember, left stage is the audience's right, and right stage is the audiences left.  If the puppeteers seem confused, tell them that they do the "Pledge of Allegiance" with their right hand and to face the audience to get their directions right.