At the moment, salary exchange doesn't work seamlessly with the auto enrolment process. You can't make an agreement for salary exchange a pre-condition for auto enrolment. However, you can choose to operate salary exchange before or after the auto enrolment process or use it as an alternative contribution basis to a default, unreduced, basis.
Alternatively, you can look into amending contracts of employment to have the same effect as salary exchange. You may need to take expert advice on salary exchange before deciding what you want to do.