Footnotes are preferred to endnotes.
Expository footnotes (i.e., those that elaborate or clarify) should be avoided as much as possible. If the information is important, it probably belongs in the main body of the text. If it's not important, it can probably be omitted.
Footnotes appear at the bottom of the page on which they are cited.
Footnotes always end with a period, even if they are not complete sentences.
Footnotes are numbered consecutively throughout an entire document, using superscript Arabic numerals. In longer documents with a lot of footnotes, numbers may be reset by section.
The superscript numbers used in the text come after any punctuation (except an em dash) and after a closing parenthesis.
He said, "There was a fire on the rig,"1 (Earlier he was on record as denying being there2—which evidently was untrue.)3
Avoid putting footnotes in the middle of a sentence. Always prefer the end wherever possible.
The company said the incident was "minor" and that it notified us as such.1 [Don't put the footnote after "minor"]
Very occasionally, a note applies to the document itself and not a particular element on the page. These sorts of general notes typically appear at the bottom of the first page and are signalled with an asterisk.