Well a simple search of the area may provide other clues. I try to date things. It helps narrow down who could have put it there. Knowing who and when helps with the other questions.
Marks at the holes could mean who put it there, and how to enter, or this case, use the hole. Its possible there is a trail out and the marks help with that or next point in the trail/puzzle. Look for at least two ways in and out.
With the daily sand storms of the area, most stuff is probably buried. You need more than just a hole. Some call them confirmation marks. Lack of any other symbols or signs could be mean you have found nothing. This also could just be a reference point for anything.
The symbols cant really be deciphered till you know who put them there.
Last, look for the nearest water source and search there for clues. If no water is visible, look for dry river beads or green vegitation.
Good Luck.