tagging a transcription consists of adding segmentation or parenthetical tags to the text. For example, it might consist of xml tags which define a constituent structure as in some syntactic treebanks.
This is different from stand-off annotation where the annotations are in separate documents and aligned in time or on the transcription by the indexation of tokens in the transcription.
It is recommended to have light tagging without excessive theoretical pretensions (the equivalent of written punctuation) which aids reading by users and automatic treatments and to separate any high-level annotations.