The best way to do this depends entirely on your situation.
FlashFXP (or any ftp client) should almost never be used to FXP files where is it important to preserve things like ownership, modification times, file system based flags and permissions, etc. However if you really had to you could create some custom commands to do it (read help file) assuming the target ftp server accepts and correctly handles the raw chmod/chown/whatever you wish to apply.
For a linux/bsd/etc system a better solution is to use the shell. tar is fully capable of preserving filesystem metadata and would be appropriate if the files are small (eg web server, text documents, emails, etc). If the files would create a tarball that is too large, or you don't have the space to store the extra tarbal, then I would suggest rsync. rsync will allow you to remotely sync from one system to another using any number of methods (ssh tunnel, ftp, remote server mount, etc) and with the correct flags will also preserve everything for you.
If you are working with windows based system then the task is much easier... simply map the network drive / remote system share / etc then cut/paste the files.
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