Can I set up an if...then... equation in jot forms

If a user clicks a box endorsing a symptom can they then get another pop up option to rate the severity of the symptom?

Yes, you can use conditional logic using Show/Hide conditions to achieve your requirement.

Do check this out: https://www.jotform.com/help/316-how-to-show-or-hide-fields-base-on-user-s-answer and let us know if it suits your requirement.