You can use WinSCP to perform this kind of automatic upload. It's normally used with SFTP or SCP but it supports plain FTP as well (your server may actually be capable of SFTP or SCP) and this can be automated with their automation scripting:
WinSCP Automation Guide
The specific command you're looking for is keepuptodate:
http://winscp.net/eng/docs/script_commands
The "Binary" transfer mode of FTP copies files exactly, byte for byte. Simple and straightforward.
When bringing text files between different operating systems, though, this might not be what you want -- different operating systems use different codes to represent line breaks. The "ASCII" mode exists for this purpose: it automatically translates all line endings from the source system's format to the destination's.
Not sure about "Auto", but I imagine it looks that the file's extension or something similar to decide whether it's a text file, and tries to guess the appropriate mode.
Which mode you want depends on exactly what you're doing with the files... if you're just copying them to back them up, then you'll probably want to copy in binary mode so they'll be exactly the same when you later restore them to the windows server again. If they need to be usable as text files (perhaps as config files for a cross-platform program?) on both sides, you'll want to use ASCII mode to translate them.
EDIT: As far as I can tell, FTPing files from Windows to Linux should never result in line breaks disappearing... however, if you copy them in ASCII mode, and then bring them back to the Windows server in binary mode, the Linux-style line endings might not be recognized on the Windows box. (Notepad won't see them; Wordpad will; YMMV with other software.)
(Today, such a convenience -- converting line endings automatically -- might seem odd in such a basic protocol as FTP. When FTP was invented, though, sending text files was the norm, and one of the goals of the protocol was to make this as easy as possible.)
Best Answer
Windows uses both a carrige return and a line feed to show the end of a line in a text file. Unix generally uses only one (I think a line feed). When you ftp files as text, the ftp program will convert line endings for you. In binary mode the file is transfered exactly as is. So if you are transfering a text document then use ASCII. Anything else and binary is probably your best bet. As others have pointed out, most modern text editors will deal with line endings anyway (Notepad doesn't, nor is it modern :) ) so binary is by far the safer option. I also agree with @njsf, I don't like files being changed behind my back. I have editors that are quite capable of doing a find and replace to fix the line endings if it becomes necessary.