As a professional editor, I see my share of:

I was helping Michael. (Brandon, always independent, did not require any assistance).

Note that there is a period following "Michael" and another following the closing parenthesis. This is incorrect--why end a sentence outside the parentheses when it began within the parentheses? Here's the correct version:

I was helping Michael. (Brandon, always independent, did not require any assistance.)

The period must remain inside the parentheses because --

• The phrase preceding it was finished, and
• The phrase within parentheses is a complete sentence.

If you are tempted to put a period outside the parentheses, you must eliminate the period finishing the preceding sentence so that both clauses are within one sentence. For example:

I was helping Michael (Brandon, always independent, did not require any assistance).

Grammatically, this is correct. (You may prefer to eliminate the parentheses and use a semi-colon instead for the sake of style, but you get the idea.)

Suppose that you wish to put several sentences in parentheses within an ongoing sentence. For example:

When putting relish on your hamburger (which should never be undercooked. Undercooking of ground beef can lead to food poisoning), don't pussyfoot around the issue--slather it on!

Here we see a period within the parentheses and the beginning of a new phrase. The second phrase in the parentheses does not require a period--the exclamation mark at the end of the whole phrase serves as the only other end-of-sentence required.

Suppose the message about food poisoning was important enough that you wanted to put an exclamation mark into the phrase, like so:

When putting relish on your hamburger (which should never be undercooked. Undercooking of ground beef can lead to food poisoning!), don't pussyfoot around the issue--slather it on!

This is acceptable because the punctuation is specific to the phrase at hand. Be careful to keep the punctuation inside the parentheses, however.

Note also that the comma follows the parentheses and is not included within. This rule conflicts with what you may know about punctuation and quotation marks. The rules are not the same--the comma must remain outside the parentheses.

Sources Used: Chicago Manual of Style, 15th ed. Section 6.103