First, Linux and FreeBSD are two separate operating systems.
Yes, you can copy your existing website through a network. In fact there are several optional methods. Either you can use Network File System (NFS) or Samba in linux to connect to your Windows network. With Samba you can share drives and printers between linux and windows clients.
Some reading on linux and administration visit:
http://www.linuxdoc.org/
and
http://www.linuxdoc.org/guides.html