@ShelleyO9850 You do so via Environment Overrides. Below are some links to provide more details. Essentially, right-click on the label of the property you wish to override in the Properties section (on the right side of the screen) and select "Environment override". From here you can add new environments and manage the values for each one.
When I deploy the project, I get one .pega file. When I run the file in Runtime, the Default environment runs. I have 3 environments. How do I specify which environment to run or how do I create/access individual .pega files for each environment to run in Runtime?
@ShelleyO9850 Generally speaking, for Runtime, you'd likely want to use Pega Robot Manager to deliver your packages. From there, you can assign the appropriate override to the user or group that requires it. If that is not an option, then to launch Runtime without Robot Manager and run with a specific EO, you would use the following command;