Setting up replication

I have a question about setting up replication between my
postgresql-9.3.6 servers. If I'm using pg_basebackup on my FreeBSD 10.1
slave server, the postgresql.conf file is in the data directory, which
pg_basebackup insists must be empty. I can't find any info about how to
relocate the postgresql.conf file and tell the init script its new
location. If I setup PITR prior to replication setup and share the same
postgresql.conf file transferred by pg_basebackup, how can both servers
see the archive directory? It is local for the slave, nfs mount for the
master.

Obviously there is something I'm missing or not understanding, can
anyone help? Thanks!

--
Robert