"I do not know whether to look."
Translation:Nevím, jestli se dívat.
Somewhat confusingly, the word that wants to be in the "second position" is not always placed literally after the second word in a sentence. It can also come after the second word in a clause, or after the second "unit of meaning" (a group of related words, like an adjective with the noun it modifies) in a sentence or a clause.
Here, se is the second word in the second clause of the sentence... so it actually does follow the "second position" rule. And, yes. the comma separates the first clause from the second.