Deploy the appliance on whatever network is available in the installer, then edit the VM network adapter settings to use the network (port-profile) on your N1KV. Then login to the appliance and apply IPv4 or IPv6 settings appropriate to that network.
I believe it also depends on what version of the appliance you are using as it took a while for some appliance vendors (even VMware's own) to support the N1KV. If you are using the latest you'll be OK hopefully.
Failing that just use normal vswitches 