FTP (File Transfer Protocol) is one of the most common ways to move files on the Internet. Characteristics to look for: resumable download, synchronize site.
I noticed that several list members recommended WS_FTP for synchronizing your directories. I, too, used WS_FTP for several years, having tried most of the others and finding them short by comparison - from WS_FTP v2 through WS_FTP v6. That was until I discovered Windows Commander v4.51 that is available from www.ghisler.com. [Hard to understand exactly what it does or whether downloaded version can be used from look at site - fs]
WinCommander isn't *just* an FTP program. Nor is it *just* a file manager. It is highly customizable. It treats network drives as if they are on your own system without the need to 'map' them - even those on the Internet.
The FTP feature is, IMHO, easier to setup and use than WS_FTP and provides a command line for direct input of FTP commands. You can have several FTP commands running simultaneously in the background and have several FTP sessions open at the same time - great for copying files from one domain to another.
The directory synchronization feature can include *all* subdirectories and will compare in multiple ways - content only, ignore date, etc. You should play around with this on your local machine to familiarize yourself with it prior to using it on your site - it works fast and permanent!
It's a 32 bit program for Windows architectures. It can be configured to work with Ifanview for graphics, NoteTab Pro (or any other text editor) for editing, DOS PKZip programs for archiving, etc. It views .zip, .arc, .zoo, .lzh and other files as folders and treats them as such when you have them associated with their equivalent DOS programs.
I consider it to be one of my most valuable utilities - right up there with NoteTab Pro - and would be thoroughly lost without it. Again, you can get it at http://www.ghisler.com/ I have no association with the site or the program except as a *very* satisfied user. Try it for yourself - I'm sure you will find it as useful as I do.