You're asking questions that are too broad, or are about less-than-established formatting. I'll do what I can though. Punctuation on quotation marks: There is one rule that is always the case.
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1. A punctuation mark goes inside a quote.
2. If the parenthesized phrase is a sentence, you put a punctuation mark in like this: (I have never been to Rome, but I hope to go.) If the parenthesized phrase is a sentence fragment, you can only put commas, semicolons, colons, parentheses, and brackets inside. You can't put periods, exclamation points, question marks, or ellipses.
3.