I use webpack path aliases for ES6 module loading.
E.g. If I define an alias for utils instead of something like
import Foo from \".
In PHPStorm (using 2017.2 currently), I have not been able to get webpack configs to work properly in regards to aliases.
My fix involves using the "Directories" section of the main settings. I just had to mark each folder referenced by an alias as a sources root, then click the properties dropdown for each and specify the alias as a "Package prefix". This made everything link up for me.
Not sure if the Directories section exists in WebStorm, but if it does, this seems to be a fool-proof method for getting import aliases working.