In general, use sparingly. The urge to use parentheses is often an indication that the sentence has become too convoluted and needs to be rewritten.
Incidental material within a sentence is best set off with commas or em dashes. If parentheses are used, place a period outside the closing parentheses if the material is a fragment: He cited the ongoing influence of the B-52s (the band, not the bomber). If the material is a full sentence, the period goes inside: Minneapolis and St. Paul make up the Twin Cities. (Although Minneapolis is larger, St. Paul is the state capital.)