"a bag" is singular, so "is" needs to be used. "two glasses" is plural, so "are" needs to be used. "of apples" and "of water" are prepositional phrases. You can remove those and the sentence is still grammatically correct and that will help with deciding which of is/are to use. "on the table" can also be removed if it helps. There is a bag. There is a bag on the table. There is a bag of apples on the table. There are two glasses. There are two glasses on the table. There are two glasses of water on the table.

the first one ( is) and the second one is ( are).