Cjkohen,
Thats' a great permit at my favorite time of year, I'm jealous:-)
You have plenty of time which means you have options. You main decision is if you want to take the easier JMT or take the opportunity to check out Clouds Rest, given the time you have it would be a shame not to experience Clouds Rest, on a clear day this is the best view in Yosemite plus it gives you the chance to look down on Half Dome to see what you are in for the next day.
In terms of planning camps it's a bit tricky because you have so much time which means you will have lots of time in camp. The good news is the bugs are not so bad in September so you should be OK camping by the lakes.
You could do something like this;
Camp 1 - Cathedral Lakes - Easy first day and a nice place to hang out especially if you have a pack raft
Camp 2 - Sunrise Lakes or on the summit of Clouds Rest, You will need to make sure you can carry enough water. On a clear night when its not too windy this is an incredible experience, if the summit is in the clouds it's not so good.
Camp 3 - Option 1 - About a half a mile before the Clouds Rest / Half Dome trail junction , there is creek that flows most of the year, this is a good camp site but there's not a lot to do or see.
Camp 3 - Option 2 - You may also want to consider Little Yosemite Valley where you can play in the river, have a good wash and use the Toilets
Camp 3 - Option 3 - On the approach to Half Dome or just below the Sub Dome where the Rangers hang out. This is a good option if you plan to do Half Dome in the evening or early morning but you will need to carry in water.
Camp 4 Little Yosemite Valley
Hike out - See other threads on the arguments for and against the JMT vs the Mist Trail