We're not talking about literally adjusting atmospheric pressure here, rather, the ambient reference pressure used in AFT software.
The default value is 1 standard atmosphere, but can be changed as desired. Open System Properties either from the Analysis menu or by double clicking the System Properties check box in the status bar, and select the System Data tab. Enter the desired value in the 'Atmospheric Pressure' field and select the appropriate pressure unit in the adjacent unit drop down box. Gauge pressures, NPSHA and cavitation calculations will reflect this specified atmospheric pressure.
Note that this does not change the value of the "atm" unit which is always a standard atmosphere, 14.69598 psia or 0.10133 MPa.