The first thing that comes to my mind would be a particular rock formation, where he piles rocks in a certain shape.
I can think of a few ways to blaze a trail from my Boy Scout days, but most of those wouldn't last long. I'm thinking of scraping bark or bending branches a certain way. Scrapes would look very natural during the deer rut, but not so much in late spring, and an outdoorsy type might notice it. "Man, that's like the third tree I've seen today with a deer scrape."
Maybe instead of the rock formation, he puts the rocks in the crook of a tree limb? And he always marks a particular species of tree on the north edge of the clearing.
Then again, there's almost certainly going to be a map made of the equipment installed. Maybe your employee has another map made showing the dead zones. He'd have to make sure the owner's map doesn't show the dead zones though.