Locally, run the installation commands to set up the template, as described in section 2.1 of the README
Generate app bundles from Studio Pro as described in section 2.8 of the native builder tool guide.
Copy the generated files from Studio Pro (bundles folder in your project directory) into your template. Section 2.2 of theREADME document in the template repo describes where to copy the bundle files and assets. (NOTE: the readme specifies using MxBuild.exe to create the bundles. You can do this but the official approach is now to use the native builder as above)
You can now open Android project in Android Studio and iOS projects in XCode as covered in the README.
Set the URL of your Mendix server appropriately. They should be set in the following locations