1. Can the quotation mark " "be used anywhwere in the beginning, in the middle or just at the end?
It's used at the beginning of the quoted part and only for the quoted part. Since this can be a phrase, it can be used anywhere in the sentence that such a phrase occurs.
2. Can the Question mark used anywhere in the beginning, in the middle or just at the end of the Sentence?
At the end of the question. Where the sentence contains two questions or more and oral inflection suggests they are separate (as in transcriptions), they are written as two sentences. Hence, it occurs at the end. Note that some questions can be short: for example, "Sino?" ("Who?")
3. Can the Acclamation mark ! be used anywhere in the beginning, in the middle or just at the end of the sentence?
In a formal situation I'd apply the same rule as for question marks. However, I've seen colloquial texts (blogs, e-mail messages, TXTs) in which cusswords, for instance, bear exclamation points in the middle of a sentence. Formally, these should be understood as parenthetical.
When you talk about punctuation at the beginning, do you mean for instance: "!Bwisit" ? That's not done. In old texts (up to the 19th century) you may see them as a result of Spanish influence, but the classical literature from that period has already been rewritten along the lines I'm explaining.
A vocative at the beginning of a sentence, like "Anak!" ("Son/Daughter!") or "Kababayan!" ("Fellow citizens!") may be written with an exclamation point. Usually, a new sentence follows, but there is literary license about this. Speech writers, for instance, may not start a new sentence to indicate that this is only a point of inflexion in a continuous idea. In this sense, it would be possible to write, say, the Our Father, beginning with a vocative of this sort. (Normally, it would be written with a comma).