This is a common scenario in many programs. You will want to document the combined class time from 3:30 until 6:00 PM as separate class(es) in the combined-class profile in your accreditation portal. The teaching staff members that lead and/or assist in the after-care class(es) should also be added to your staff profile in the accreditation portal.
When it comes to the Class Portfolios, you may create an addendum to your existing preschool and/or kindergarten Class Portfolio(s) that includes documentation for the types of activities and materials the after-care class(es) are doing and using, if not already documented there.
Hopefully this answers your questions however, please feel free to reply again if you have follow-up questions.