I found out the same thing when bowhunting deer how the squirrels would run around and not be bothered by you being in a tree stand. So I tried it. I put my tree stand in early and hunted squirrels until I decided to hunt deer.
You set up in that tree stand and it just dosen't bother them, because there is no movement on the ground and no noise of you walking through the woods.
I used a portable stand so I could move around. Early in the morning get set up and wait for sun rise, and watch the squirrels run around. Also later in the afternoon is a great time.
When you shoot one, just leave it until you are done hunting then go pick then all up at one time. You may need a pencil and paper to keep track where they are....
Try it you will enjoy it and I think you will see more squirrels..that way you have them coming to you instead of you going to them.. that way they don't even know you are there....good luck...stump