If you're happy you're happy, but if you're using Maven and you're mixing sources and resources and using unconventional directory structures, you're only setting yourself up for more problems down the line.
I can't tell you what to do, but I can advise you that you can fix now what doesn't seem broken before it gets too complex to fix when it IS broken.
I challenge you to the following, it shouldn't take much more than 15 or 20 minutes of work: Copy your entire project folder to a safe place, and then delete all Eclipse files and all generated files from your original project folder, so you're only left with a Maven POM and a src folder. Make sure that the src folder has the following structure:
You life will become MUCH easier if you put resource files in a package with the same name as the package that the source files are in that will be using those resources. For instance, if you have a class com.example.gui.MainForm, you could have the following files:
Now, in Eclipse go to the File menu, click Import... and then browse to the Maven folder and select Existing Maven Projects. As the root directory, select the directory above your project directory, and Eclipse will find all Maven projects inside that directory. Select your project and finish the wizard. Eclipse will now create a completely new Eclipse project that has all the correct settings according to your Maven POM.
In the <properties> element of your Maven POM, add the following element:
In the <plugins> element of your Maven POM, add the following plugin:
Now go to the Run button and instead of clicking it, fold it open and select Run As... > Maven Build... (with the ellipsis at the end. In Goals, enter clean install exec:java, and then when you run your project with this build configuration, it will build and run in with Maven, which is definitely what you want if this is a Maven project.