The original sentence is:
In which, I am wondering if I should insert a comma after "You":
Which one is more correct, and why?
Both can be correct.
It depends on how you want to say it. Do you want a pause after you or not? In other words it's up to you. Use the comma to represent a pause in speech. Omit the comma if there is no pause after you in the speech you are representing in written form.