No, for information security and data protection reasons, you cannot edit the structure of the Checkout.com Secure File Transfer Protocol (SFTP) directory for reports.
The SFTP folder structure for each report is specified under the Report format section on the dedicated report page. For example, for the Payouts Report, the report is uploaded in the following folder structure: {Entity_name} > reports-{Entity_name} > payouts.
You can then manage downloaded reports in your own storage location.