I'm not sure exactly what you're asking, but if you want to tell Qpopper to look in a different directory for the spool, you can use the 'spool-dir' option in a configuration file. (I think you can use this in a user-specific configuration file if you want, but the configuration file has to be in the default spool directory, and I'm not sure that scenario was tested, so try it first.) See the Administrator's Guide for more details.
You can also use the '--enable-spool-dir' option with ./configure. Try './configure --help' for a full list. All of them should also be in the Administrator's Guide, but I think a few were left out by accident. --