“Not only… but also” can serve as a connection between clauses that make sense as sentences individually, or when the second clause is an independent clause. In such cases, it is appropriate to use a comma.
“When cooking, Frank uses not only the kosher salt, but he also includes the table salt.”
– “Not only… but also” can be used to connect nouns as well. In such cases, it is wrong to use a comma, especially when the second clause is a dependent clause.
“His favourite instrument is not only the recorder but also trumpets and trombones.”