Setting up an HE tunnel on a Debian box is pretty straightforward. Just set up the Tunnel like normal in your HE portal and put the following configs in your /etc/network/interfaces file
auto he-ipv6
iface he-ipv6 inet6 v4tunnel
address $HE_IPV6_IP
netmask 64
endpoint $HE_ENDPOINT
local $LOCAL_IP
gateway $HE_IPV6_GATEWAY
ttl 64
Next time you reboot your machine or restart the network you will have interface he-ipv6 for your tunnel interface.