My suggestion is to set up a Samba server. the smb protocol allows you to transfer files between a windows and a linux machine. It can also be password protected, which is good!
Do you happen to have a copy of the Red hat Linux 8 Bible? if so, that has a REALLY good section on getting your samba server running.
The basic steps to it are:
1. install samba on your server and clients. make mount point on your clients, eg #mkdir /mnt/samba
2. Edit your config file on your server (/etc/samba/smb.conf). When I get home tongith, I will post mine, it is VERY basic as I'm only sharing some files.
3. Add samba users. In order to add samba users, the users must already have an account on your server. Do this: (skip first two lines if the already have an account)
#useradd -m bob
#smbpasswd -a bob
<enter same password as above>
Start samba on all machines:
On linux, you can mount the remote filesystem like this:
#mount -t smbfs username=bob,password=<password> //<server IP>/bob /mnt/samba
On the windows box, it should just appear in the networking (i think, but I have never tried).
Hope this at least points you in the right direction. As I say, i will post my smb.conf tonight. In the meantime, google around and find out a bit more about the smb.conf file.