Multisite installs on that note, only put custom mods in sites/all/modules/custom if they are being used by more than one site otherwise put them in sites/all/sitename/modules/custom the same can be said for custom themes although, I ve never heard of them having custom and contrib in themes it s sufficient to put master themes in sites/all/themes and custom themes in sites/sitename/themes if using the libraries module put your libraries directory into sites/all so they are available everywhere There s one GOTCHA you should be aware of, DON T name your module the same as your theme.