If the subdirectories you created are qtrees, and you want a different export policy for each one, then you can use the following command to apply a policy to each individual qtree.
Otherwise, each directory within the volume ,whether it is a qtree or just a folder, will use the export policy of the parent volume.
Unfortunately you can't apply the policy to the qtree in system manager. You would have to use:
qtree modify -vserver *vservername* -volume *volumename* -qtree *qtreename* -export-policy *export_policy_name*