I read about one method (but not done it myself) which is you work out how much reveal/offset your face frame will have Vs the inside of the cupboard. E.g. on the bottom, your face frame might be flush, so it's the same offset on both the frame and the carcass. If at the top of the cabinet, your face frame over hangs the inside surface of the top of your carcass by say, 5mm, then you add 5mm to the fence height when you cut the mortice in the face frame. So basically, always reference the inside surface and work out the offset based on the amount of overhang of the face frame.
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