Question: My last publisher wanted every thought in Italics, even if it said "she thought" afterward, though that part of the sentence was not in Italics. You said that doesn't get any Italics. Yet SOME thoughts get Italics even after you edited the manuscript. I looked through some books on my e-reader and some had Italics and some didn't. I'm still confused....
Answer: Different publishing houses choose different rules. There is a typesetting rule that says half a sentence cannot be in Italics, though there are exceptions -- if, say, half the sentence is the title of a movie, that WOULD get Italics. So the rules can differ from publisher to publisher. But if you are working with us, or any publisher who used the Chicago Manual of Style, the following should be correct.
But the rules of grammar say that Internal Dialogue gets no Italics and direct thoughts get them. If we go strictly by the rules of grammar, then if "she thought" isn't in Italics, the rest shouldn't be either. But that's only half the story.
In fiction, there are two kinds of thinking:
Internal dialogue: where the character thinks to himself or herself in Third Person, in the voice of the character. This technique originated most notably with Mark Twain and got him lots of criticism in his day. Here's an example of Internal Dialogue:
Ellie threw herself into the chair. She was sick and tired of the way she was being treated. She thought
they had better watch out or they might hear more from her than they wanted to!
Clearly, above, we are in narrative, but also in Ellie's thoughts. It is in Third Person, not a direct thought, but still couched in the character's voice, and none of it gets Italics. This is an example of Internal Dialogue.
Direct Thoughts in First person: get Italics. For example:
Ellie threw herself into the chair. I am sick and tired of being treated like this!
The Italics indicate it's a thought, so there's no need to say "she thought," afterward. That would be redundant. Where most folks go wrong is to add a "she thought" AFTER "treated like this!" above. The sentence is in First person. I am sick and tired.... First person makes it a Direct Thought from Inside the Mind of the character. To add a "she" in third person within the same sentence creates a disagreement in person.
Internal dialogue gets no Italics. Direct thoughts get Italics.