Where does "emphasis mine" go in a quotation?

I have often seen the term emphasis mine used whenever an author wishes to denote that emphasis in a given quotation originates from said author rather than from the original source.

What is the proper place for this phrase?

One possibility is immediately following the emphatic text, inside the quotation. But, see next question...

What if there are multiple emphatic sections marked within the quote?

If "emphasis mine" comes immediately after each phrase, it would end up repeated two or more times, which seems a bit messy. In this case, would it be OK to place "emphasis mine" at the end of the quotation? If so, should it be inside or outside?

How should the phrase "emphasis mine" be set off?

I believe I have seen parentheses () or brackets [], though brackets are also used to indicate words added by the one using the quotation.

Wikipedia's Manual of Style, similar to most other style manuals, says:

Do not put quotations in italics unless the material would otherwise call for italics, such as for emphasis and the use of non-English words. Indicate whether italics were used in the original text or whether they were added later. For example, directly from the Manual of Style:

"Now cracks a noble heart. Good night sweet prince: And flights of angels sing thee to thy rest." [emphasis added]

What I found most subtle among the different methods I've seen was to put it right between the introductory text and the quotation itself, between parentheses. Like so (emphasis mine):

Whatever.

In this way, it's easy for the reader not to focus on that if he doesn't care, and to be aware of it when actually reading the quotation if he does.

I wouldn't call that a rule, but I don't think there's much more but good practices adressing this question either.

In French¹, I stumbled on the interesting other technique of embedding this information in the surrounding text. Translating² :

[…] : « [book extract] Maintenant, […], blaguons… »³

Balzac emphasised that, then to comment : “[…] dazed, as it could have been hearing an angel blaspheming.” We emphasized that.

The author highlights Balzac's comment, but I'm the one who highlights the way he inserts it in the text.

¹ in which I don't see many such notices, because emphasis is seldom added, I reckon.
² It's about the etymology of “blague” (→blaguons), hence the importance of that word being emphasized by the original author.
³ Italics for being foreign ommited for the sake of it all.

As a general rule-of-thumb, place "(emphasis mine)" immediately after the quotation.

"As for you, you were dead in your transgressions and sins" (Eph. 2:1, emphasis mine). (Bowland)
Not: "Uneasy (emphasis mine) feelings, feelings of compassion ... (emphasis mine)"

Where there are many sections that you emphasized and probably extended over several sentences, or even paragraphs, you can, alternately, place it at the beginning of the quote, preferably with a terminal colon. "(emphasis mine:) Uneasy feelings, feelings of compassion ... "

When there's already an emphasized part within the quote, place "(emphasis mine)" immediately after the part that you have emphasized.

"According to the pragmatic view, the proper goal of science is to augment and order (emphasis mine) our experience." (Cory) -- The word 'augment' was already in italics in the original; 'order' is being emphasized by you.

The most common practice seems to enclose the phrase "emphasis mine" in simple parentheses: "(emphasis mine)" -- where there's a possibility of ambiguity, you can switch to square braces, "[]". However, one needs to be consistent throughout in the convention.