Autopods tracks the git repository of your pods and automatically triggeres a pod install when needed (e.g. when you change branches). The pod install will only be triggered when it is actually needed and you would get an "out of sync" error in Xcode anyway.

If for some reason the pod install command fails, the error will be displayed together with a button to spawn a Terminal window in the pods folder.

If you need to manually run pod install or pod update, you can use the dock menu to trigger that.