According to several writing conventions, (including MLA Style), when a writer wishes to emphasize a particular word or phrase within quoted text, (s)he can use an offset font (usually italics), underlining, or bolding, proceeded by the phrase "[emphasis added]" within square brackets.
I pledge allegiance to the flag of the United States of America, and to the Republic for which it stands, one nation under God, indivisible, with liberty and justice for all. [Emphasis added]
One only needs to add the notation of [Emphasis added] when emphasis has, in fact, been added. If the original source is in writing, and already has bold, underlined, or italic text, it is just as important to include the notation, [emphasis in original] to avoid any confusion.
It's a bit more ambiguous if the original source was verbal. If you are quoting someone's spoken words and you think they imparted into their own speech the verbal equivalent of bolding, underlining, or italicizing, it is, IMHO, justifiable to include this emphasis with a bracketed notation such as, [Emphasized as such by the speaker].
If the quoted source is in writing, it is best to maintain the original author's bold/underline/italic emphasis along with the [Emphasis in original] tag, but if you choose to eliminate the emphasis because of editorial limitations or other reasons, you should include either a bracketed tag saying [Original emphasis excluded], or else a footnote explaining the same.
Obviously, if the inclusion of bracketed tags calling attention to the absence of emphasis would be even more distracting than including the emphasis itself, then either opt for a footnote, include the author's original emphasis, or, as a last resort, go ahead and corrupt the quote by just getting rid of the emphatic style. It may be frowned upon by those who purport to know better than me, but it happens all the time.
While it is a best practice to avoid adding emphasis to another person's text, sometimes emphasis is critical to making a point. So even readers who find it distracting will be forgiving if you've added emphasis carefully and necessarily.
Remember, the [Emphasis added] tag is only for quotes. There's no need to include it when using emphasis in your own text.
When adding emphasis to quotes in an E2 node, keep in mind that using the [ and ] will automatically create hardlinks, so use the codes &#91; and &#93; to create left and right brackets, respectively.