I used to use FileZilla, but now is an FTPRush fan. Just remember some sites takes longer than others before FTP uploads shows. SS is very fast, while some other sites can take up to 24 hours. If my FTP client indicated a successful upload, I do not re-upload unless 24 hours have passed, to make sure that the process is not just slow (else, as you experienced, double uploads).
Start perhaps putting your images in batches and keep track to which sites you have uploaded which batch. This will help you with the duplication problem, till you are more used to the process.
Best of luck further.