Q. How do you show emphasis (and not with capital letters) in “thought” that’s already in italics?
A. If you must put thoughts in italics (italics are just one option among several), emphasis is usually shown by “reverse italics,” like this:
Does this mean no more waffles, like ever? That’s bad, very bad, I thought.
But you probably wouldn’t have written to us if regular type in an otherwise italic environment worked well as emphasis. Compare the same text but in reverse:
Does this mean no more waffles, like ever? That’s bad, very bad, I thought.
Readers are likely to miss the regular text in the first example (or to notice it but not understand it as emphatic); they are less likely to miss the italics in the second. But if you really want the words to stand out, try bold text or underscore (if your publisher allows it):
. . . That’s bad, very bad, I thought.
. . . That’s bad, very bad, I thought.
Underscore may be the better option. Thanks to the legacy of typewriters (and handwriting), it’s already understood as an alternative to italics. Bold, on the other hand, tends to jump off the page wherever it occurs, which could be either distracting or perfect, depending on the desired effect.
In sum, you have several options, among which is the option to use regular text for thought, reserving italics for emphasis.