The RIP configuration resides in
ripd.conf.
Quagga uses one daemon/process for each routing protocol, and they all communicate with the
zebra daemon which in turn manipulates the routing table.
zebra.conf should only contain interface IP address assignments and static routing. Usually, the init system handles that on Linux, so
zebra.conf can be left more or less empty.
I would suggest you consult the
documentation for more detailed information.