I'll give you a pointer, not a complete HOWTO.
Usually it is recommended to write a bash script to do whatever you want to do, and call the bash script from cron. In my signature there is the URL of the Bash Scripting manual, in there you'll also find some tips for converting DOS scripts to Bash scripts. If you do only file copying it is very easy.
Then, I assume you have some Samba drives mounted in your Linux machine. You either want to backup from a Windows machine to a Linux machine, or from a Windows machine to another Windows machine.
If you have mounted your Samba drive on the Linux machine, you mostly find it back in /mnt, so:
Once the drive is mounted, you'll find the subdirectories there.
A copy action is something like:
cp /mnt/server2/blue/* /mnt/server1/blue_backup/.
from one Windows machine to another, or
cp /mnt/server2/blue/* /home/backup/blue_backup/.
to this Linux machine.
However, for backups etc, it is much better to use rsync. You can use rsync locally, that is from one drive in the file system, say /mnt/server2/blue, to another mounted drive, say /mnt/server1/blue_backup
rsync is very powerful, and has a zillion modes and options. Do check the man page and run a few tests before you bring it in the production environment.