First, consider the organization of your sonnet.  If you are going to write it in Shakespearean form, then you would start with three  quatrains (four line stanzas) and end with a couplet. 

Much of Macbeth is about appearance vs. reality, particularly that sometimes characters may have the appearance of goodness, but on the inside they are evil or wicked.  For example, Lady Macbeth's lines to Macbeth before Duncan's arrival:

bear welcome in your eye,
Your hand, your tongue; look like the innocent flower,
But be the serpent under't. (I.7.69-71)

In the first stanza of your sonnet, you could introduce your theme of "foul is fair..." and the idea of sometimes things not being what they seem. 

Perhaps the second stanza should be dedicated to something seemingly fair, and you could use personification and imagery to portray it beautifully, like an apple.

Then in the third stanza, you could reveal that the beautiful apple is actually rotten to the core, or has a worm in it. 

Then in the final couplet, you could revisit your theme, and maybe add your own twist.