Go to your server.cfg on the file manager page and edit it. Add the following to the top of your server.cfg:
seta sv_punkbuster 1
Then restart your gameserver and punkbuster should be enabled.
A more detailed one can be used as well:
seta sv_punkbuster "1"
wait // This is required for proper PB startup
pb_sv_enable // If you want PB disabled, use pb_sv_disable instead