Go for the three stage option, it makes perfect sense. Remember as well as six sittings, you are only allowed four attempts at any one subject. So if you have sat all exams by the third sittings, that still leaves three sittings for resits, that still gives you the maximum number of attempts(four) at any subject. So you will not lose anything by using the third sitting, you will only increase your chances of passing all at first attempt.
For the record I did distance learning on a three stage ground school and got every subject at first attempt.