If they be two, they are two so As stiff twin compasses are two;
Once again, Donne attempts to cut off any and all counter-arguments, just in case some jerk wants to bring up the fact that, as nice as it is to talk about being "one" and everything, they still are literally two people who are going to be separated by hundreds of miles. So the beginning of this line concedes a little bit: "Fine. We're two. But if we are two…"
He immediately whips up a new metaphor, one as weird as any we've seen yet. Nothing says romance like mathematical equipment, right? In this case, Donne begins to draw comparisons between he and his wife and the two legs of a compass.
The metaphor works with Donne's theology well enough. Even though the legs of the compass are separate parts, they have been joined together permanently and are useless apart from their partner.
The repetition of the word two in these two lines is to slowly begin to redefine the term. You've heard politicians subtly shift the meanings of words to suit their argument. Same thing's happening here. He admits that he and his wife are two, but then redefines two to mean what he wants.
Thy soul, the fix'd foot, makes no show To move, but doth, if th' other do.
We are reminded here that this is a poem written from Donne to his wife. It's easy to forget because the argument becomes so convoluted, but the "thy" brings us back to his audience.
Donne's wife is "the fix'd foot" of the compass, meaning the one that stays planted in the center of the circle.
Donne begins to establish the quality he finds so vital in his wife—her constancy. She is not only the fixed foot, but she "makes no show to move" until he (the other foot) does. She is completely faithful to him and supports him in whatever he does.
It's easy to read this in the 21st century and say that this is Donne emphasizing his wife's need to stay at home and depend on him for everything, and we guess that's true enough. But try to remember that, given their age and culture, this is still an impassioned praise of a woman's love.