If you use and work through the program in interview mode the way it is designed and intended to be used, it is practically impossible for depletion to not be taken.
Elect to EDIT your royalty property in the program, and the third or forth screen in shows the default depletion amount (default is 15% of the amount you entered previously) and you can even change that amount if necessary.
Then, if you elect to update Expenses you'll see there on the "Enter Common Expenses" screen the depletion amount in the box labeled "Depletion".
