With the latest version, the Live Update will issue a NOTIFICATION there's an update available, but it will be always your choice whether to apply it or not. A check for update is made automatically every 24 hours, or manually if you select the "Check for Updates" option.
And, the Live Update will recognize the kind of update. If it's a minor one, it can apply it without requiring to quit the sim, otherwise (if any of the executables changed), it will suggest to quit from the sim and run the Live Update from the Desktop icon.