File & Folder Permissions

Hi does anyone know how to set the files & folder permissions in an sc application, before it is zipped up for production.
I deploy to 2 servers one is ok with permissions as set by sc, the other will not open the production UI unless all the files and folders are set to 755 (error 505)
The first time I deploy to this server I had to change recursive, using ftp program and this takes a while to complete.
Thank you