The Basic PAYE Tools software isn't really fit for purpose when it come to automatic enrolment as it can easily go wrong.
My suggestion, if you are able to, is to switch to a commercial software provider. Some would supply it for free for 1 employee and this would usually include the assessment, communications and submissions for you.
Everyone will have a different opinion about the software to use. HMRC have a list of the free ones at https://www.gov.uk/payroll-software/free-software