I tried to find this rule explicitly on several grammar sites, but did not find it.
A "not only" sentence does not normally need a comma as the "not only" and "but also" are correlative pairs. So "Not only does he like cheddar cheese but also mozzarella" does not need a comma.
My question is what happens if the "but also" clause is in the middle of the sentence, such as:
Not only cheddar cheese but also mozzarella cheese is really good on Triscuits.
Should there be a comma after "cheddar cheese" like so
Not only cheddar cheese, but also mozzarella cheese is really good on Triscuits
or maybe also after "mozzarella cheese" like so
Not only cheddar cheese, but also mozzarella cheese, is really good on Triscuits.
I'm not sure which way seems to leave either clause less incomplete.
Best Answer
Edwin Ashworth's advice in a comment above is very sound. There is no standing rule requiring writers to split up a "not only ... but also ..." construction with a comma—regardless of where that construction falls in a sentence—and in many instances the sentence will be better off without the extra punctuation.
The only categorical exception to this recommendation (again as Edwin says) is when the components of the "not only" and "but also" components are so long that readers may lose sight of the controlling structure without a comma to signal the break between the "not only" piece and the "but also" piece.
So of the OP's three options, I think that the first is the most sensibly punctuated:
If you don't like the syntactical awkwardness of that sentence, however, you should feel free to switch to the simpler wording endorsed in user114275's answer: