I'm sorry, perhaps I haven't had enough coffee this morning. Your post makes no sense to me.
You need to setup your DHCP server, either through the router or use Piholes DHCP to point exclusively at Pihole as it's DNS source. If you manually put an DNS entries in a device and specify anothe routside DNS server it will use it when it can. The terms of primary and secondary (and tertiary) mean nothing at all any more. I think at least in Windows it USED to mean "take them in this order". Now it just means 'use them all'.
So, if you have ONE Pihole, set your DNS to it only. If you have TWO Piholes running, then make sure both are specified in your DNS list. It should hit one or the other and effectively split your DNS traffic.