Following are the steps to override folder clean settings for a particular domain from smartermail.

1) Login into SmarterMail as admin.
2) Search your desired Domain Name from the search box.
3) Right click on Domain Name->Click on Manage.
4) Expand the filtering->Click on Folder Auto clean
5) Select Radio Button against override auto-clean settings for this domain.
6) Click on Folders from menu bar (if it is already created).
7) Set your desired Auto clean folders settings.
8) Click on save button.