Several things play key in that equation. One of them is the distance between your boards. The second is the settings you are running on your setbacks.

As a rule of thumb, I run all of my baits from outside to inside. The longer leads go to the outside with the shorter to the inside. This way, when you trip the board, the bait is already behind the one closer to the boat.

If you are running setbacks really similar right next to one another, I prefer to stager my boards futher from the boat. This puts that outside board further away on the triangle. Think geomotry and a 90 degree isosoles triangle!!!

Another trick is, when you trip the outside board, let the bait and board fall back for a little while before reeling. This will ensure you are not reeling in your baits overtop of one another. Same when you have a fish on. No harm in allowing the fish to pull the board more towards the middle. Just ensure to keep pressure on them.

Some people will tell you the opposite. They will tell you to go shallow to deep so that you can pull the bait overtop of the inside board. This is however WRONG! I don't say that too often but these are the guys you will hear saying "I only have one or two tangles". Always go by setbacks regardless of depth the bait is running. Here is an example:

I am running three different baits on one side of the boat. A Rapala DDHJ 12, a size 9 Berkly Flicker Minnow, and a Reef runner 800. I want all these baits to run around 15 foot deep. My outside board would be the Rapala set at 80 feet back. My middle board would be the Berkley set at 65 feet back. My inside board would be the reef runner set at 49 feet back.

If you do it like some say to do and run the reef runner on the outside you would be pulling it across 90 feet and 65 feet of line out!

So, always go by setback with ONE exception! If you throw bottom bouncers in to the mix, always run your crank baits OUTSIDE of your bottom bouncers. Same for tadpoles.

This is done differently however if you are running lead core. For lead, you run your deepest diving baits on the INSIDE. So, if you were running 10 color, 7 color, and 3 color your outside board would be the 3, the middle would be the 7, and the close one would be the 10. This is were the confussion comes in when guys tell you to reverse your setup.