In "The Good-Morrow," there are a few dual pairs, all about love. The most obvious dualism is between two kinds of romantic love: physical love and spiritual love. And these two manifestations of their love is described in terms of being in two separate worlds.
The first dualism is between the past and the present. The poet suggests that the world of his and his lover's past is like another world when compared with the present. He supposes that before they met and fell in love, each were both babies or figuratively asleep (the Seven Sleepers den refers to a legend of a cave where persecuted Christians slept for 700 years). He even suggests that all supposed acts of love and sex ("country pleasures") that occurred before they met were nothing compared to the love they have now.
In the second stanza, the poet says that he and she are both worlds in themselves and together they make one unified world. Contrasting this idea with the larger world (Earth) of explorers, the poet gives greater significance to his and her individual worlds and their life together. This sets up a dualism between the individual and the earthly world.
The most significant dualism in this poem is between earthly love and spiritual love. He prefers the hemispheres of their faces to the hemispheres of the Earth. "Whatever dies, was not mixed equally;" means that whatever is made out of earthly stuff is limited by the laws of physics and can't be mixed completely. Their spiritual (and emotional) love is metaphysical, meaning "beyond" the physical and therefore, not subject to the laws of nature. Existing beyond those laws, it can't die, it is immortal.