I cannot test with Server 2008, but the following should work:
To add a tunnel from command line, run
netsh and type:
add v6v4tunnel Tunnelbroker localaddr=<local_v4_address> remoteaddr=<tunnel_v4_endpoint>
add address Tunnelbroker address=<client_v6_endpoint>
add address Tunnelbroker address=<routed_prefix>:1
add route ::/0 interface=Tunnelbroker publish=yes
add route <routed_prefix>/64 interface="Local Area Connection" publish=yes
set interface Tunnelbroker forwarding=enabled
set interface "Local Area Connection" forwarding=enabled advertise=enabled
<local_address> with the server's IPv4 address (the external one in your case with PPPoE, internal if the server itself is behind a NAT).
<tunnel_endpoint> with the IPv4 address of your tunnel's server endpoint (given in the Tunnelbroker tunnel info page).
<prefix> with your tunnel's IPv6 "Routed /64" prefix, for example,
2001:470:1f0b:614:: (given in the tunnel info page).
This only configures IPv6 Stateless Autoconfiguration. After the tunnel is created (the first 3 commands might be enough), you should be able to create DHCPv6 scopes in the DHCP management console. Someone who can test it on Server 2008 should expand this part...