Typically people use Qtopia Desktop to sync between the Zaurus and your main machine. I never however managed to make Qtopia Desktop looks good, i.e. using the antialiased font rendering. Beside, it is just much easier to use Kontact (with its Kitchensync) so that your PIM data is integrated with the rest of KDE.
But how to transfer documents? Well, just use the powerful kioslave of KDE. Since Opie is running an FTP server on port 4242 (forget first the security implications), you just need to type:
in Konqueror, then you will (after got prompted for password and confirmed in the Z side) have access to the Compact Flash card (CF) content. Bookmark this, and you never have to type and memorize that long address again.
Since my digital camera also uses CF, I also don't need to search for that camera USB cable anymore (one less to care for). Just pull the CF from the camera, plug it into the Z, then copy my pictures conveniently. I still hope Krita runs on Z one day :-)
Even more interesting, you can work directly on that folder. For example, when I use Z to jot some notes and save it as a text file in CF, later on I just dock my Z on the cradle, click on my CF-on-Z bookmark, open the text file with KWrite, type some content, then save it again. No hassle.
The power of kioslave has been often demonstrated. In this particular use, it allows me to skip the download-edit-upload or sync-edit-sync steps. Nice, isn't it?