At the moment, salary sacrifice doesn't work seamlessly with the auto enrolment process. You can't make an agreement for salary sacrifice a pre-condition for auto enrolment. However, you can choose to operate salary sacrifice 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 sacrifice. You may need to take expert advice on salary exchange before deciding what you want to do.