I havent tried it myself and there was no reply on below suggestion that I think could work:
Tail the logs live to see whats happening when you connect a device to either segments:
sudo tail -F /var/log/pihole/pihole.log | grep dnsmasq-dhcp
EDIT: Oh I noticed you'd might want to advertise a different router IP for the second subnet.
Then it should be below if eth1 were the second interface name ... as an example:
$ sudo nano /etc/dnsmasq.d/99-my-dhcp.conf
# Subnet network2.dehakkelaar.nl
domain=network2.dehakkelaar.nl,192.168.2.0/24,local
dhcp-range=eth1,192.168.2.50,192.168.2.250,24h
dhcp-option=eth1,option:router,192.168.2.1