Instead of writing everything in question I would like to place an image. The problem is where should I place the resource directory which contain the .properties files?
See the image for more information and exact problem.

First of all, if you are using Intellij IDEA and Gradle, try adding this to your build.gradle:
apply plugin: 'idea'
idea {
module {
inheritOutputDirs = true
}
}
The more likely solution
From my experience Java 9 has locked down accessing resources based on some rules about whether the resource is encapsulated or not (see javadocs).
Things that have worked for me:
Putting a resource in the root of my resources folder and calling
getClass().getClassLoader().getResource("myresource.txt")
Making the folder structure leading to your resource match a suitable package in your project. For example, if you had a com.your.package then your folder structure would be resources/com/your/package/myresource.txt. Once your had this, you can add opens com.your.package in module-info.java and get your resource by calling
YourClass.class.getResource("/com/your/package/myresource.txt")
Other things to try
Marking your resources folder as resources in Intellij IDEA.

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