Not sure if you are setting the DNS in your Fritzbox in the WAN section but this usually is set in the DHCP DNS, so clients will get both DNS while getting the ip address and not all DNS queries going through the router and then to the pihole....
On the other side, yes this will not be balanced as is working as intended. Clients will query any of the configured DNS, but normally hitting more queries in the primary (although you are saying that your secondary is getting much)
You can sync piholes using gravity , setup this as High Availability i.e. with keepalived (google for more info....so only 1 pihole would be active at the time) or simply leave the 2 piholes set in your DHCP DNS configuration.
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