Hello,
YES even with dual stack you will still need to configure tunneling for communications between two IPv6 islands..over IPv4 cloud.
Options available in dual stacking mode are :-
1. Manually configured tunnels [pt to pt]
2. GRE tunnel [Pt to pt..Can carry CLNS traffic too for IS IS too..!]
3 Automatic ipv4 compatible tunnels [DEPRECATED..pt to mpt, Cisco recommends using ISATAP tunneling instead]
HTH
Vijaya