Well, I can't tell where you downloaded them to, but something like this, (in xterm): cp /full/path/to/claws-mail_fix-date.tar.gz /home/user/ Of course, you can move (mv) instead of copy (cp).
Hmm, hard to say, since I boot my n800 off one of the SD cards, and I can't remember what the default behaviour was. Probably the file manager is either opening /home/user/ or /media/mmc1/
(IMO, it is not very clever that the default file manager attempts to hide the directory structure, but that's another matter.)