You can format your SD card on the zaurus by entering the following commands in the terminal : 

umount /dev/mmcda1 
mkfs.vfat /dev/mmcda1 
mount /dev/mmcda1 


However you schould check first if /dev/mmcda1 is your SD card by typing 

cat /proc/mounts 

the output should look like this : 

/dev/root / cramfs ro 0 0 
/proc /proc proc rw 0 0 
/dev/ram1 /dev minix rw 0 0 
/dev/mtdblock1 /home ext2 rw,sync 0 0 
none /dev/pts devpts rw 0 0 
/dev/mmcda1 /usr/mnt.rom/card vfat rw 0 0 

This works fine with a Embedix version 1.0 (see System Info for that)