Hi Helen,
There are several ways you could try and tackle this but perhaps the quickest is to create recurring invoice templates for each customer on the Sales>Invoices>Recurring menu. Each template can be set up with a payment on recurrence at the bottom of the form:
Instead of using the imported statement to reconcile these transactions, you could do this much quicker by manually reconciling:
https://support.clearbooks.co.uk/support/solutions/articles/33000203298-manually-reconcile-bank-account
The alternative would be to create an import rule for each customer payment on the Money>Import rules menu. The search term for each rule would need to be the unique customer reference number.