If you're not cruising, it's smart to be aware of when ships are scheduled to show up. If you're planning to visit outlying sights or beaches, do it when the ships are in port — by the time you return to town in the afternoon, the cruise-ship passengers will be loading up to leave again.
Whenever you visit, enjoy your time here and simply give yourself over to the Greek islands. With a few exceptions, the "sights" (museums and ruins) are not worth going out of your way for — you're here to relax on the beach and explore the charming towns. Make the most of it.