Technically you don't have to do either, as the Airport will pass packets regardless of what's in them (IPv4 or IPv6). The key is making sure the Airport is in "bridge" mode rather than router mode. In Airport Utility, this is on the second page (Internet) and is under "Connect Using" and "Connection Sharing". You want:
Connect using: Ethernet.
Connection sharing: Off (Bridge Mode)
This will cause the Airport to pass packets directly from the E3000 on it's Ethernet port to the wireless network and vice versa.
As far as IPv6, Airport routers don't have "IPv6 off" mode. To be fair, nothing with IP should have IPv6 off mode at this point as too many people just ignore it if you can turn it off, but I digress. The closest thing to "off" is "link-local", which means, "negotiate yourself an address on the LAN that is only usable on the LAN". So... you don't want "link-local".
You want "host" mode with "configure IPv6" set to "automatically". This will cause the Airport Express to pick up a V6 address from the E3000 and use it for itself, while still allowing V6 to pass through it in bridge mode.
Hopefully Apple chooses to update the Airport line at some point to actually make them work as routers when connected to native IPV6 DSL... but for now, this is the hack we all have to use.
Hope this helps.