These are two different usages.
In the waiter question, the answer is that it depends on how the waiter views the situation. If he views it as two separate orders, he can certainly say 'waters', and this can be used for any other drink order as well, 'the beers' 'the whiskeys' 'the sarsaparillas', whatever.
On the other hand, if he views this as one order for the general commodity 'water', I think he might well say 'the water'. I think this would work for non-liquids as well, 'the spaghettis' vs. 'the spaghetti' seems equally possible, but the orders must be for the exact same thing.
Frost's poem 'Directive' is a different story. 'Waters' here is actually in a sense listed in Merriam-Webster's 3rd International, which gives four different meanings for 'waters':
'a natural mineral water': "He drank the waters for rheumatism."
'the water occupying or flowing in a particular bed': "the limpid
waters of a mountain brook"
'a portion of water for a particular use': "Wash the greens in three waters"
'the marine territorial waters of a state': "The ship was in British waters."
The reference in the poem is to the story of the 'holy grail', which has several versions; in one popular version the grail is the cup Jesus drank from at the Last Supper. If you drink water from this, the story goes, it will have a magical effect, which varies from story to story.
So which sense do you think fits here? You have five minutes.