I don't know if there really is a "proper" way, but here's how I counteract that smudge you are talking about.
Rubbing alcohol works fine, but after you clean it, before you put it in the lens nut you should do one final swipe, straight across the lens, this will wipe all the little tiny particles to the edge where they will not be in the way of the laser beam.
Its very important you do it in one smooth motion, as every time you stop or change direction you leave behind micro particles that come off of any type of fibers or cloth, even microfiber.
Blowing it with a little compressed air after that wouldn't hurt either.
Blow it from the side, you should wipe and blow everything in one direction, so that the particles stuck on the lens due to static cling will at least be at the edge where they are not blocking the beam.
That's what I do, it seems like everyone has their own lens cleaning methods though.
