grammar - Where, if anywhere, do commas belong in a "not only... but" sentence in which the "but" clause appears in mid-sentence?

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:

Not only cheddar cheese but also mozzarella cheese is really good on Triscuits.

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:

Both cheddar cheese and mozzarella are really good on Triscuits.