Buddy Punch will track any type of time via a punch in and a punch out. The time between a punch in and a punch out is defined as a "shift" in Buddy Punch. You can assign labels such as Department Codes (like Job Codes) and Locations to shifts.
For paid breaks you can create a department code called "Paid Break" and "Regular Time" and assign it to an employee. When an employee goes to punch in they'll need to select between the department codes that you assigned to them. When you run a report on types of time you will see this time broken up by Paid Break vs Regular Time so it can be tracked accordingly.
Please note that Automatic Breaks are not types of time such as Department Codes or Locations but instead a way to automatically punch an employee out and back in during a shift. Therefore automatic breaks do not apply to paid breaks.