(Newport Beach, CA,USA)
Question: When a character in the manuscript is thinking, should those lines be in quotation marks?Answer:
That's one option. The trouble is that you often want to distinguish a character's thoughts from dialogue - or any words spoken aloud.
Because dialogue is always in quotation marks, thoughts are generally put in italics in a printed book. In a manuscript, the standard practice is to underline any words that should appear in italics in the printed book. (This practice began because manuscripts used to be written on typewriters that did not have an italic font.) Some publishers today prefer you to choose an italics font in a word processed manuscript.
Occasionally you will come across books where the thoughts are printed just as regular text and other books where they are in all capitals, though these are less effective options.
The safest course is to underline thoughts and save quotation marks for dialogue.