Running package-installed eggies can add some complications compared to compiling it yourself, mainly as you need to make sure you load modules from the proper location among other things..
Usually, you would place a copy of the distribution configfile in the home directory under which your eggdrop is intended to run under (and no, eggdrop will not run as root, don't try to run it as a service).
Once copied, you'd modify it taking caution with settings related to shared files (modules, helpfiles, etc), while setting userfile, channelfile, etc to be created within the home directory.
Of course, you could create a subdir under your home directory and use that instead.