@Sameer Shemma
For your trick to work does one need:
- to only add this new folder .coffeejs and change the single line that
you highlighted in the watcherTasks.xmlfile or
- to replace my entire watcherTasks.xmlfile by yours?
I tried to first possibility and WebStorm would still not stop at most breakpoints put in the .coffee files. 
For the second I did not know what would be the correspondence of the "/usr/local/bin/coffee" path value of the name attribute in my case (Windows 7, Meteor 1.4.1.2, CoffeeScript package 1.11.1_1, WebStorm 2016.2.3), but without changing that, WebStorm still does not stop at most breakpoints put the the .coffee files.
Also, does your trick do require to install a CoffeeScript file watchers and/or stand-alone compiler outside of the one presumably included in the Meteor CoffeeScript atomosphere package 1.11.1_1 that I am using?
Here is my current watcherTasks.xml file:
<?xml version="1.0" encoding="UTF-8"?>
<project version="4">
  <component name="ProjectTasksOptions">
    <TaskOptions isEnabled="true">
      <option name="arguments" value="--output $ProjectFileDir$/.coffeejs/ --map --compile $FileName$" />
      <option name="checkSyntaxErrors" value="true" />
      <option name="description" value="Compiles .coffee files into .js files" />
      <option name="exitCodeBehavior" value="ERROR" />
      <option name="fileExtension" value="coffee" />
      <option name="immediateSync" value="true" />
      <option name="name" value="CoffeeScript" />
      <option name="output" value="$FileNameWithoutExtension$.js:$FileNameWithoutExtension$.map:$FileNameWithoutExtension$.js.map" />
      <option name="outputFilters">
        <array />
      </option>
      <option name="outputFromStdout" value="false" />
      <option name="program" value="$ExecutableByFileExt$" />
      <option name="scopeName" value="Project Files" />
      <option name="trackOnlyRoot" value="true" />
      <option name="workingDir" value="$FileDir$" />
      <envs />
    </TaskOptions>
  </component>
</project>