In general, you should place a comma before a conjunction only if it links two independent clauses.
Sally bit her brother, and she smacked him on the head.
Sally ran to the ice cream truck and hit the driver.
Sometimes, a comma should also be used for clarity.
He thought she had lit a candle and started to cry.
He thought she had lit a candle, and started to cry.
My question is, should a comma be used for clarity after a conjunction when it's preceded by a list?
Our afternoons were spent baking cookies or cupcakes or visiting the bakery.
Our afternoons were spent baking cookies or cupcakes, or visiting the bakery.