This only applies to accounts with a Reserved IP block. If your account does not include reserved IP space, this does not apply to you.
Your /48 IPv6 allocation is routed to your VLAN as a /64; use addresses within the first /64 subnet (::1 is the gateway). Reserved IPs are assigned to your account, not to any particular service; you are free to use any IP from your reserved blocks with any server provisioned with reserved IP space.
Why only a /64 by default?
A /64 is sufficient for practically all use cases. Assigning more than 2^64 addresses on the same VLAN is wasteful, and the full /48 is held in reserve should your needs grow.
Routing the entire /48 (advanced)
Customers with multiple hosts or services (VPS instances, dedicated servers, etc.) may need to subnet the /48 into several /64s and assign them independently. For those customers, we can route the entire /48 over a link-local address (fe80::/64). This is standard practice per RFC 3177 and RFC 5375.
This is an experts only option. We assume you know how to configure your end of the link and will not provide additional support for it. If you cannot get it working, we will revert to the default /64 setup.
To have your entire /48 routed over a link-local address, please open a support ticket.