I dont know if one direction is better than the other. I run DNA filters, and they stick out approx 1/2 to 3/4 of an inch, and there is NO way they can be installed backwards. I do know of people that have installed and run the K&Ns backwards....and have not said there was a difference in how the bike ran....but....speaking with Tim Nash, if they velocity stacks dont move up and down, it will COST approx 10 hp up top, so after they are installed, I would put the airbox back together, and leave the main filter out (so you can see) and if the velocity stacks are moving up and down when you turn the key on and off. For me, even with grinding on the inner lip of the right DNA filter, the right front velocity stack would still catch just a tiny bit, so I had to grind perhaps a mm off the outer edge of that stack.
The velocity stacks are supposed to be able and move up and down approx 1/2 and inch. You can see if there is a difference with NO airbox on vs with the airbox on, and main filter out to see.