How are you doing it? You can just drag the header file or you can chose to read the header file from IB. The class won't show up anywhere in IB until you create an object and assign it as your custom class. Such as if you are subclassing NSWindowController, you read your class header file and you drag a controller from the tool pallet thing. In this example you would drag an NSObject into your nib/xib and in the Identity tab for that object you set it's class to be that of your custom class.
IB 3 is different than 2.x because you can't create your classes in it now. In IB 2.x you could subclass NSObject and instantiate it, but IB 3 you no longer do this. All of that is done in XCode.