Pay attention to vocal inflection. When they raise their voice asking question, you know to add a question mark after. When they pause, it could be a comma or period. There could be a raise in the voice to indicate an exclamation mark or even all caps. You should know enough grammar to add what is needed and hopefully you can do most of this while taking dictation so you end up with good notes when you transcribe (typing up what you took down).
The importance of this is illustrated by the following words:
"that that is is that that is not is not is not that it it is."
This groups of words is absolutely meaningless if uttered without pause or inflection in the voice. But if the sentences are pronounced as they are written in the following manner, there is no question to their meaning:
"That, that is, is. That, that is not, is not. Is not that it? It is."