Punctuation is a matter of style, and as such you should be governed by your manual of style, either the one you've chosen or the one thrust upon you. I prefer The Chicago Manual of Style, but whichever one you choose realize that the there will always be allowance for the author's necessarily subjective judgment.
CMS notes that when it comes to punctuation, form follows function, and that said function has three components: to clarify meaning, to aid the reader, and to contribute to style. There are two schools of thought -- close punctuation (which supplies the marks to follow the syntax as much as possible) an open punctuation (which supplies the marks only in those cases of possible "misreading.")
Close style will always recommend and open style will usually concur that coordinated independent clauses be separated by a comma unless the the clauses are very short:
George washed and Martha dried.
In the given example, a middle-of-the-road style will thus recommend that the sentence have a comma preceding and and following the dependent clause:
He is very particular about his food, and if it isn't cooked to
perfection, he will send it back.
Close style will bracket the dependent clause with commas:
He is very particular about his food, and, if it isn't cooked to
perfection, he will send it back.
This looks choppy, and even in 1982 when the 13th edition of the CMS was recopyrighted, this style is noted as somewhat out of favor.
A strong open style will omit the commas in the second clause or even omit all the commas on the grounds that a markless sentence won't lead readers into misparsings.
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