This is a trivial problem.
Use a config file per protocol to keep it easy. For us
perdition.pop3.conf for example regulates only the POP3
protocol (port 110). Off the top of my head picking out what I
think are the relevant changes we made from defaults:
# ssl_mode MODE[,MODE ...]::
# Use SSL and or TLS for the listening and/or outgoing connections.
#ssl_mode ssl_listen
ssl_mode tls_listen,tls_listen_force,ssl_outgoing
pop_capability TOP LOGIN-DELAY 180 UIDL USER STLS SASL PLAIN
listen_port 110
outgoing_port=995