Yes, FSAutostart will restart all of your services when you exit Sh3. I've set it up so that FSAutostart loads SHCommander, which then starts SH3.
Best to start with the default settings. You can adjust if needed. The configuration screen has some info about each service to help guide you about which to terminate. You may need to tinker with it a little, but it hasn't crashed my computer yet, so you shouldn't have any probs.
