I'm not sure if I understand the problem correctly, but disabling transfer to temporary filename may solve your problem.

If i log in to my server as "root" and SFTP, and upload/edit some files/folders,
Then the normal user can access those files and folders when he log in to his own account with FTP...
Because those files/folders has "root" access and the user cant do anything because of his own "user" access.

How can i solve this problem. I dont want WinSCP change the owner of files/folders when i did something as root.