The great thing about staying in a resort in South Atoll is the opportunity to snorkel with whale sharks. The snorkeling in South Atoll is usually better, but that may depend on the quality of your particular hotel's reef. During my first trip to Maldives, I split my time between two hotels. I personally enjoyed experiencing two hotels for more variety in meal options and water activities. If you are spending more than one week there, then it might be worthwhile. If you are spending only one week, then the cost of flying from one hotel to another might not be worth it. You would have to fly from your hotel back to the capitol of Male and then from there fly to your second hotel.