By far the best way to visit Greece is to take a flight only into Athens then take the one hour bus ride to the port Piraeus. Have a mental list of islands you wish to visit - use the many ticket agents to find a conveniently timed ferry. Outside the period mid-July to end of August finding accommodation is easy as people will meet incoming ferries. In Naxos I recommend Hotel Galini in Naxos Town. Other islands worth visiting, which can be reached easily from Naxos, are Syros, Amorgos, Folegandros and Donhoussa. Read a good travel book before you go!
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