On the Project -> Design Condition screen you can manually override summer and winter outdoor design temps. The program will provide the 5 closest weather stations to the address entered on the project screen. If you select the one with the closest altitude, you can then override the temperatures if they are not accurate or a local code requires specific temperatures to be used. If you create a ticket with us we can help identify the station with the closest altitude to the address. We tend to stick with the weather station data in the ACCA Manual J book and not allow custom weather data to be entered because more than likely the user would not know the additional information we need, like design grains at various relative humidities. 

It's important to note that altitude has a relatively minor effect on the total cooling load. Every 2000 ft reduces the infiltration, ventilation, and humidification loads loads by approximately 6%. However, higher altitude climates tend to be dryer, so infiltration and ventilation cooling loads are often low, making the overall impact fairly negligible.