oh sorry, i misunderstood.
to make custom network interfaces in the container you can make PVE ignore it:
http://pve.proxmox.com/pve-docs/pve-admin-guide.html#_guest_operating_system_configuration
like
touch /etc/.pve-ignore.interfaces will make PVE not modify the interfaces file and your changes should be kept.
be aware that most our ubuntu containers use systemd-networkd to configure networking