Application updates
Installing remains your call.
PalCommand checks roughly once a day unless you turn the check off. Before an app update installs, running servers are announced to, saved, and stopped carefully. Stable is the default channel; beta is opt-in.
Uninstalling
What removing PalCommand deletes.
PalCommand never deletes anything outside its own data folder, so server installs, saves, and backups kept in a location you chose are always safe. The uninstaller has an optional checkbox to also remove PalCommand's data folder, which is where server installs, saves, and backups live by default if you never moved them. Leave that box unchecked to keep everything at the default location.