Bill,
There will be a thousand different answers to this one.
I usually put the faster of two engines in the second position. My reasoning is this. If the faster engine is in front it is pulling not only all the cars but also the heavier load of a slower engine. Look at this arrangement going up any grade and watch for wheel spin on the faster front engine. This will only burn out the motor eventually
If the faster engine is in the second position it is basically just pulling the cars and sometimes pushing the slower engine which is actually pulling its own weight and helping pull the cars some of the time. This results in a little "bump and grind" of the two engines, but not so much that it is obnoxious.
Now if there are three or four engines in your lash-up, I put the fastest in the rear again. Same reasons as above. But the key is, if the engines are too far apart in speed, nothing you can do with position will help. You will have to slow down the faster one with a resistor on the motor or some other electrical method.
One more thing. Stick to the same brand and model engines to run together if possible. Different manufacturers have different gearing and different models also have different gearing from the same manufacturer.
Pete