The following characters can be used for non-ascii characters of Sumerian or Akkadian transliterations:
š: c or sz
ṣ: s, (with comma) or S (upper case)
ṭ: t, (with comma) or T (upper case)
The cuneiform output can be copied into a word processor (e.g. Microsoft Word). However, in order to see cuneiform signs there, a cuneiform font must be assigned to this text in the word processor. If you don't have any cuneiform font installed on your computer, you can get it from here (ORACC) or here (K. Šašková, Pilsen).