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qpopper is very good... install it and run the server and Linux/Unix does the rest! Actually, if you think about it, Unix systems (Unix clones of course) have the best indigenous (or is homogenous a better term?) set up imaginable (users and security) but I digress...
should be installed in /usr/local/bin... since its a service youll have to go to /etc/rc.d/init.d and look for something like pop3 or a binary that looks like it.
the best thing to do would be to use the man pages and this will tell you how to start it. When i used it last year, i had a very standard mail server and didnt have to make one bit of configuration to it.
I just looked for it in /usr/local/bin and /etc/rc.d/init.d and it wasnt there. I dont have anything in /usr/local/bin. But I did 'locate qpopper' and i found it in /etc/log.d/conf/services/in.qpopper.conf and I also found qpopper names in /etc/log.d/scripts/servoces/om.qpopper. Does any of those look like it would be instead of the two files that you named?