The Speaker will call you when it is your turn to ask your question:

If you have the first question say “Question 1, Mr Speaker” and then sit down. When the Prime Minister has replied to the engagements question, stand and ask your supplementary question.

For subsequent questions, there is no need to say the number of the question. When the Speaker calls your name, simply stand and ask your question.

You can watch a video of the most recent Prime Minister's questions.