Not sure this is the official way, but it could be done by putting a dotted line under the word, and writing /stet in the margin. Stet is Latin for 'let it stand' and is normally used to remove an alteration - but it would do just as well in this case, I think.

How I've heard it's done is while you go through it with the editor, he will make notes and adjust spelling and grammar to suit the book. Most likely, purposeful miss-spellings happen during dialogue, where people tend to drop the "g's" off of the end of words as in, "He was smellin' the fish fry on the bbq..." etc.

1) "Nevertheless, it is reckless to assume that an author does not know what he is doing. The revised typescript for “The Captured Shadow” has a note in Fitzgerald’s hand: “Please follow all spelling throughout, even when wrong.” The instruction refers to passages from the juvenile hero’s writings, which include deliberate Fitzgerald misspellings. Such evidence provides a corrective to groupies who find gratification in the image of Fitzgerald as an irresponsible (i.e., drunk) writer who spontaneously generated flawed masterpieces." " Fitzgerald is regarded as an orthographic phenomenon on the basis of his manuscripts (“yatch,” “apon,” “facinating”); but he not unreasonably expected proofreaders to do their jobs. Because of the scores of misspellings and usage errors printed in This Side of Paradise (1920), Fitzgerald’s career was launched with the stigma of irresponsibility that remained attached to him and has influenced editorial thinking about his work. Wilson described that first novel as “one of the most illiterate books of any merit ever published (a fault which the publisher’s wretched proof-reading apparently made no effort to correct).”17 Assessing the extent of Scribners’ responsibility for textual details is crucial to establishing policy for re-editing Fitzgerald. Wilson’s application of illiterate is hyperbolic; nevertheless, Fitzgerald never developed the habit of accuracy. His sense of direction was unreliable, and his arithmetic was approximate especially in calculating the ages of characters. These handicaps do not diminish his genius which did not depend on navigation or mathematics but they blemished his texts and provided ammunition for detractors. Fitzgerald was not indifferent to the errors in his published work and their effect on his reputation. In 1920 he urged Perkins to provide corrections for the London edition of This Side of Paradise, and in 1938 he proposed a new edition of the novel with a “glossary of absurdities and inaccuracies." Source and further information: http://www.sc.edu/fitzgerald/essays/right.html 2) "Innacuracies. Transcribe an inaccuracy, misspelled word, or misprint as it appears on the material. Follow such an inaccuracy either by “[sic]” or by the abbreviation “i.e.” and the correction within square brackets. " "Do not correct words spelled according to older or non-standard orthographic conventions, e.g., “françoise” for “française,” or “antient” for “ancient.”" Source and further information: http://dcrmg.pbwiki.com/f/0-DCRMGv2.0.doc