(-> Thanks to energiequant.de!)
OK, now for the details. I got Zen working with Amarok 1.4.8 running on a current sidux. And I guess that's the point: you might need rather current versions of programs and libraries. sidux being based on Debian sid does provide all this. If you're running Ubuntu Gutsy you might need to compile some of those, but I can't tell for sure. Just try.
You need of course Amarok and libmtp7. I additionally installed mtpfs and mtp-tools, but I think you don't need those. I guess Amarok is part of nearly any Linux distribution, so you may need to add libmtp7. In case of sidux/Debian/Ubuntu (as root):
apt-get install libmtp7
Ubuntu Gutsy comes with libmtp6 and I cannot tell if this works with this version of libmtp. (EDIT: libmtp6 does not work!) You might need to install the current version from this website or wait for Hardy... I might try this on my notebook running Gutsy - if so, be sure I'll let you know! Once libmtp7 is installed, connect your Zen to a free USB port an start Amarok.
Go to Settings -> Configure Amarok -> Media Devices and select Add device. Choose MTP Media Device as module and give the new device a name. You don't need a mount point. Now select the Media Device tab, click Connect (see picture) and you should see your media library.
To upload tracks, go to your local media library, right click tracks or albums and send them to your media device. Those tracks will be queued and are transmitted by clicking the button next to the Connect button. And as bonus: if you let Amarok manage your album covers, those will be visible on your Zen!! (A feature I missed with Zen's Windows software.)
Before disconnecting your player, be sure to click the Disconnect button!
That was easy, wasn't it?!?