How to punctuate "A and B and C" properly if "B and C" form a set

You can write the matched pair with an ampersand instead of the word and to indicate that they are closer than the other items in the list:

We ordered spaghetti and fish & chips.

This usage isn't universal, although Wikipedia notes some specific cases where it's preferred:

In film credits for stories, screenplays, etc., & indicates a closer collaboration than and. The ampersand is used by the Writers Guild of America to denote two writers collaborating on a specific script, rather than one writer rewriting another's work. . . .

The ampersand can be used to indicate that the "and" in a listed item is a part of the item's name and not a separator (e.g. "Rock, pop, rhythm & blues, and hip hop").

If you're working with a particular style guide, it may have advice on whether ampersands are preferred (or forbidden) for these kinds of cases.

The only way to do it as it stands is A, and B and C. Whether that would be clear enough depends on the context. If it wasn't, then you might want to think of some other way of putting it.