I don't believe there is a special mode support for that via the file manager. You might just try to upload it and see if it works - as many FTP clients are smart enough these days to figure that out on their own. The file manager might be the same. If that doesn't work for you then I would suggest trying to upload with a FTP program instead as that would give you the flexibility you need.
The same could be said with chmoding a file, except I know you can do that via the file manager. All you need to do is click on the link for the file in question, then click on the "Change Permissions" link.