While the various product are more or less different flavors of the same program, if you want do work on a polyglot project the best choice is probably Idea since is the more flexible. The others have a better out of the box experience for a specific language but have a few limitations here and there.

For example (and if I remember correctly), Webstorm doesn't support a project with different modules, so if you want to split it in two or more parts you have to either create it with Idea and "import" it in Webstorm, or manually edit the project file.