In Web Report Designer, you can save report into Report Server using the publish option.
publishoption in top-right corner of enterprise server page.
Publish As Reportdialog.
Publishbutton to save the report.
If you are saving the report with duplicate report name, it will as confirmation to replace the existing report,
Yes to replace the report or
No to edit the report name in the name field.
If you are editing a report from server, the
Publishoption will directly replace the report into
Refer the Download report section to download the published report from server.