I didn't really get what your problem is. Are you running eclipse from within the USB Stick or are you trying to access the USB Stick through an eclipse instance that was run from your hard drive? If the second one is the case, then check if you have even mounted the usb stick.
If you don't, try running the following as a root: mount -t vfat -o rw /dev/sda1 /mnt/usb (i'm assuming here that sda1 is your usb stick and you have an empty directory called /mnt/sub)
If you want to save again to the usb stick, you have to edit your fstab and give permission to a normal user to mount filesystems, try changing the line referring to the usb device in your fstab to something like this:
dev/sda1 /mnt/usb auto noauto,users,rw,umask=00 0 0
or look at the
fstab tutorial in linuxquestions