In cases where a writer is quoting published writing that in its original form includes parentheses, the same punctuation marks should appear in the quotation:

Two centuries ago William Hazlitt remarked, "The English (it must be owned) are rather a foul-mouthed nation."

In cases where oral language is being quoted, readers might interpret a parenthetical expression as being an interpolation--especially since parentheses are used to signal interpolations in AP newspaper style. Consequently, it's best to use parentheses only when the words they contain were spoken as quoted but the sentence is so complicated that special punctuation is needed to clarify meaning:

"I've always felt--and you can quote me on this--that the ugliest (not to say most damaging) aspect of the electoral process, aside from the volume of paid political advertising it generates, is the rancor it encourages between people of fundamentally similar political views," Professor Squeegee said.