msys for Setup provides the following steps.
Refresh - msys for Setup will parse the existing configuration and collect data.
Customization - where you update the configuration using the customization panels.
Update - msys for Setup will use the customized data and create new configuration files in MVS data sets.
Commit - msys for Setup will update your current configuration to point to the newly created configuration files.
For port reservations, you may select to have your existing profile updated during the Commit phase. If you select Yes, msys for Setup will update your profile's INCLUDE statement to point to the newly created ports configuration file. You may decline this function by selecting No.