Desert towns were normally river towns, a smaller settlement could form at an oasis and you have coastal settlements, there is desert nearby but in general they are not "desert towns" as we all need water.
Navigating the desert isnt the big issue, a bigger problem is water or lack of, in particular when you are going to war.
Bob Brier talked about this in "The Great Courses: The History of Ancient Egypt" from 1999.
When going across the Sinai to invading the middle east they had outposts with water storage built along the way further and further out as a preparation before the army got going.
This is a great example of the good administration in ancient Egypt that managed to accomplish so much.
Brier also claimed that the vast desert of Sahara was never really in Egypts control and it was mainly a nomadic area which on occation launched attacks or raids on Egypt.
At times the Nile forks change and that have more often than not caused towns to get deserted, this was the case with the somewhat recently found Pi-Ramses.

Now middle eastern cities along the silk road is a slightly different matter and may have other answers to this.