Here is another method I use.
I have 4 directories, with 4 further subdirectories underneath each. Sometimes I want to upload lots of files in dira/subdirb and so on, therefore my original batch method is not effective.
So here's how I get around that.
The dir structure on the server is identical to the windows structure
All you have to do is to us PKZIP / WINZIP to zip the dir and subdirs then just ftp the ZIP file.
This has two advantages, 1) the subdirs are intact - you can have 1000's of files in different dirs, 2) the upload will be a lot quicker and it's easier for dropouts.
On the server, all you need to do then is to gunzip / untar but I use Linux version of PKZIP.
Of course, the other beauty is that if your subdirs has 1000's of files, but not all of them change each day, then you set the ZIP prog to just include 'changed' files.