The council, perhaps via the HR committee, should manage the clerks working schedule and leave allocation.
Are you asking because nobody is doing it and nobody knows what hours are worked, when leave is due / taken / outstanding? That seems to be a common situation and it also seems commonplace that clerks will take advantage of the peculiarities of their employment to exploit such information and management deltas.
If, as an individual Cllr, you cannot reconcile to support the salary liability when presented, vote no for payment and when enough cllrs realise they have absolutely no idea what they are voting for maybe it will bring the necessary change…