A reader writes to ask:

How should I differentiate the character's thoughts from the rest of the narrative? Some people have suggested I put them in quotation marks, but I find that when I read novels in which the character's thoughts are in quotation marks, I initially think they're speaking rather than thinking. I have seen novels in which the thoughts were italicized, but I know it's not advisable to use italics in a manuscript you're submitting to an editor. Should I instead underline all the thoughts? It makes for long underlines, but maybe it's the best way. What do you think?

There are three basic ways of indicating literal thoughts in narrative: setting them off in quotes, setting them off in italics, and not setting them off at all:

"I have to get out of this place," John thought, "if it's the last thing I do."

I have to get out of this place, John thought, if it's the last thing I do.

I have to get out of this place, John thought, if it's the last thing I do.

Each method has its adherents, and you're free to choose whichever one you think will help you make your prose as clear as possible. I'm with you on the quotes—I find it too easy to mistake those thoughts for dialog—but my own personal stylistic preference is for the third method. I find that italics gives thoughts such a strong literal flavor that seeing this technique employed often breaks me out of the story. I don't know about you, but rarely do I find myself thinking in complete literal sentences. (Except when I'm writing)

But I'm something of a cantankerous reader. I think it's safe to say that the italics method is the one most commonly used these days. It's a solid choice, and if you go that route, do not be afraid of long chunks of underlining. You are correct to avoid using italics in your manuscript; it's just too easy for editors to overlook when reading your submission, especially in Courier font. Underlining is the correct and accepted method for indicating italics in a manuscript (as demonstrated in the second example above), and no editor is going to blink at encountering a long string of it. That's what she's accustomed to seeing, even if it looks graceless to your eye.

I've written more about italics in the entry Italicizing long blocks of text.