Trolling Direction

Is it best to troll into, with, or across the waves?

Yes.
It is easiest to troll with the wind/waves. But there are times where you will get more fish going across or into the wind/waves.

I have caught fish in all directions and I have gone dry in all directions. I first prioritize the lines cooperating, then focus on finding the right speed. Often times you must adjust GPS speed (SOG) to account for current. I have a paddle wheel speedometer as well that helps me determine that. But that is just surface current. I'm anxious to get a fish hawk connected so I can see what the speed of my tackle is at the depth of the fish. Perhaps I'm over thinking it.
Good Luck!

I will always start out going with the waves. but if I find a school of fish I will turn around and fish back through the school going against the waves. if I catch more fish going one direction over the other i'll pick up my lines and motor up and keep trolling the best direction to catch fish. i'll keep working the school until they quit biting or I get my limit. but you have better boat control going with the waves.

Thanks for the comments.