new options for the directadmin.conf for file uploads in the filemanager:
fm_owners=|USER|:|GROUP|
fm_file_permissions=644
fm_dir_permissons=755
Thos are the defaults.
You can change them to things like:
fm_owners=|USER|:apache
fm_file_permissions=640
fm_dir_permissons=750
if you have suPhp.
However, although you can change |USER| to something else, I would not advise you do. You'll likely end up with permission problems if the user can't read his own files.. but for those who know what they're doing, the ability is there.