Having worked in a room that allowed running it twice, I would suggest using the following rules if you decide to implement it:
Running it twice is only allowed when players are all-in.
*All players in the hand must agree to run it twice. You may consider only allowing it when there is a heads up pot, although as long as all players are in agreement I am for allowing it in multi-way pots.
*Only allow running it twice on Pot Limit Omaha and on larger No Limit Hold'em games (depending on the size and play of your room, this could be $2-5NL or $5-10 NL, but def not $1-2NL.)
*You may also consider only allowing the running of the only the turn and/or river twice, and not the flop, in order to save time... although I think the whole board should be allowed.
When you get to the actual time to run the pot twice, you should just run the board out with burn cards like you normally do, then go through the same procedure again from whatever point the players agreed to run it twice. SO if they get all-in on the flop then you would burn, turn, burn, river. Then push up those cards and burn, turn, burn, river again. Probably better not to split the pot until you need to, because if one person wins you can save time and push him the whole pot. If it is a split, then just chop it up evenly, odd chip left of dealer or to the first hand, either way just pick one.