First, I have to say that the correct way to do an underlined number is to use the 5-step modification method. In special circumstances, for an individual student, you can probably make accomodations. Some people use the boldface indicator to designate an underlined number. If you use the boldface indicator, then you must insert the numeric indicator before the digit that follows so that the boldface doesn't extend through the rest of the number. For very young students, I have used a transcriber's note to say that the underlined digit is given in parentheses following the number. e.g., (the first 9 is underlined) I don't know if this is any help to you. Let me know if it is not and maybe we can figure out something else.
Dorothy answering for Betty Marshall