I'd like to upload only modified files (and not all files).

You have to :
1. generate your Web site in the same directory as before : so only updated files will be modified,
2. upload only recently modified files, by checking the option "Transfer only modified files within last x minutes" in the FTP dialog box.

NOTE : be careful with images, which dates can be older than you think (creation or modification date). Be sure to transfer the whole site at least once (do not check the previous option the first time).