Either way is easily doable.
Code:
/usr/bin/rsync -W --delete-during --stats -avrpPe ssh /* root@computer-to-be-overwritten:/ --exclude=/etc/hostname --exclude=/var/lib/mysql --exclude=/etc/network/interfaces --exclude=/etc/lilo.conf --exclude=/etc/grub.conf --exclude=/etc/raidtab --exclude=/etc/modules.conf --exclude=/etc/fstab --exclude=/etc/modules --exclude=/etc/lvm* --exclude=/etc/udev/rules.d/z25_persistent-net.rules --exclude=/proc --exclude=/sys --exclude=/dev --exclude=/boot --exclude=/etc/sysconfig/network-scripts
I may be forgetting a couple excludes there, but that is the gist of copying a system to a system over an encrypted ssh link. You basically want to exclude anything that would be more accurate on the new host, modules, fstab, and directories that don't make any sense to include-- proc, sys, dev, etc.
If you wanted to say just sync the vmfiles themselves you could do that by just specifying the source and destination as the correct locations.