Put full stops, question marks, and exclamation marks outside a bracket at the end of a sentence if the text is part of a sentence, and inside the bracket if the text is a full sentence.
Part of a larger sentence:
Our welcome email will explain how you can add more choices later (and if you paid a reduced fee, you will need to pay a further £11).
The text stands independently:
Our welcome email will explain how you can add more choices later. (If you paid a reduced fee, you will need to pay a further £11.)