You didn't say what kind of sailing you're planning on doing. The Gulf Islands and San Juans are probably not going to give you any trouble regardless of how your lines are led. If you stay in waters with little fetch, heading up on deck will feel very safe.
The main difference is that you will have to give yourself more time than you otherwise would, since, autopilot or no, you're giving up some control when you leave the cockpit. So just plan ahead and stay the hell away from shore and you'll be fine