Is it permissible for a charitable endowment (Waqf Khairi) for living parents—which is a monthly deduction from one's salary—to be a single sum with the intention of dividing it between them, or must it be two separate sums, one for each of them?

The monthly deduction for the poor is an act of charity (sadaqah), not an endowment (waqf). A waqf is the detention of an asset and dedicating its usufruct. If the money will be spent on buying or building something whose asset is detained and whose usufruct is dedicated, then it is a waqf. It is permissible for it to be a reward for the parents, and it is permissible to intend to divide the amount between them, because deeds are judged by intentions.