I connect mine to the rest of my network via wireless. It fetches a dhcp from my wireless router, and can surf the web without problem.
As for connecting to my other linux machines, the Z can host an FTP server and telnet server, but I've opted to use use sshd. This permits me to ssh, sftp and scp both in and out for file exchange. I've setup smbmount on the Z to connect to my mp3 server, so it acts as a portable player while connected to the network.I've never used the death-star cradle, as ssh/samba seem to be the easiest way to move things around.
Installing software is pretty straight forward: point the Opera browser to:
http://www.killefiz.de/zaurus/Seems to be the most comprehensive software index. Most of the stuff works well on the 6000.
Download files and use the internal install tool.
Note that you won't be able to install onto your SD card unless you format it with ext2. I've done this and it works well. With some careful symlinking you can setup the sd card as an extension of internal memory (essentially moving /usr/local/* and other directories to the sd card). Do that at your own risk though, I started a thread covering that topic a while back detailing how I did this.
let us know how it goes
-T