How do you let you mum-in-law know that you will be calling the shots on the upbringing of your child (without sounding rude)?

Listen to your MIL first. It wouldn't hurt having someone giving you advice on how to raise your kid. Especially this person is not a stranger. If your POV is contradicting with hers, acknowledge her opinion (respect), let her of know your POV and make her feel that you will still stick with your rules. For you not to sound rude, let her know that her son totally support you on how you will raise your kids. Win-win for both of you!