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This is what I do:

A tip, if you have a lot of folders in your online filemanager:
If you have multiple domains/subdomains that points to it's each own folder, you can use this approach.
Example:
The virtual host "blog.myname.net" points to the folder "myname_net_blog".
The virtual host "forum.myname.net" points to the folder "myname_net_forum".
The virtual host "images.myname.net" points to the folder "myname_net_images".
The virtual host "shop.myname.net" points to the folder "myname_net_shop".
Should ease the browsing in the filemanager that you know which host is pointing to what folder.
You can use dots (.) istead of underscores (_) to separate names.
The virtual host "blog.myname.net" points to the folder "myname.net.blog".
Also the folders will group nicely together by domainname with subdomainname at the end.