Compiz Fusion is just a set of plugins fr Compiz. Your best interest is to have them found both by Compiz and by Compiz Configuration Settings (also in Compiz Fusion distribution). By default they look in Compiz installation path and in home directory. You do not need to track /nix/store manually - everything is already in /var/run/current-system/sw/share. $HOME/.compiz/plugins should contain plugins you want to load. All the installed plugins are available in /var/run/current-system/sw/share/compiz-plugins/compiz/, so you can use symlinks to this directory. $HOME/.compiz/metadata should contain metadata (definition of configuration options) for plugins you want to load. All the installed metadata is available in /var/run/current-system/sw/share/compiz/, so you can use symlinks to this directory. Probably a way to load GConf configuration backend by default should be found, but if you run Compiz with GConf configuration (default for X server job for now), you have to link /var/run/current-system/sw/share/compizconfig/backends/libgconf.so into $HOME/.compizconfig/backends directory. Now you can launch ccsm and configure everything.