Great question! You are correct that you typically do not want to harvest in your bees first season in their hive. How your hive will look next Spring depends on what you leave them with for winter. A lot of Warre beekeepers will want to reduce the number of boxes they are using going into fall and winter. You will want to remove any dead space from the hive to help increase your bees chance of survival. This typically means overwintering a healthy Warre colony in two to three boxes depending on your colony's size and stores.
In Spring you will most likely want to go ahead and add the forth box back underneath to allow them to continue to draw out new wax for your brood chamber. Most of the honey stores your bees made for the winter will likely be used up and empty comb will be available for your bees to put new nectar in. Bees will naturally segregate their brood nest from their honey stores. The upper boxes, during strong nectar flows, will most likely be all honey stores. These are the boxes you would harvest from. During mid to late spring watch your colony closely, as you may need to add an additional boxes to ensure their is room for the often heavy tree blooms in mid spring.
Typically we recommend one harvest of your honey and that is in late summer early fall, Labor day weekend is usually a good time to harvest. Occasionally you may be able to harvest in late Spring if you have had particularly good nectar flows. I would consult local beekeepers in the area to see when your nectar flows are the strongest and how frequently they harvest.
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