If it is server for CB matches, use CB Configs.
Otherwise go to www.pbbans.com/mci.php , save cvars to file pbsvcvar.cfg , md5 tool list to pbsvuser.cfg and upload them to server's pb folder.Then execute over rcon pb_sv_load pbsvcvar.cfg and pb_sv_load pbsvuser.cfg
All pbucon settings should be in pbsv.cfg.
You don't have to use jPAT to update ban lists anymore unless you're streaming via hub and pbucon profile is 1 . You should set pb_sv_AutoUpdBan to 1 as well.