In Akkadian context, there are basically two ways to “read” a given sign:
(I): a logographic reading; the values are inherited from the Sumerian period. In this case, the sign will be transliterated in capital letters.
(II): a phonographic (or syllabographic) reading; the sign represents the pronunciation of a syllable in either the Sumerian or Akkadian languages. In this case, the (phonemic value of the) sign will be transliterated with small letters.
It seems that in the phonetic reading case, the transliteration system does not distinguish between the Sumerian and Akkadian origin. That is, no matter the sign is representing a Sumerian or Akkadian pronunciation, it depicts its value using small letters. If this is the case, for example, the reading tu_6 can basically represent either an Akkadian or a Sumerian syllable. Am I right?