By some reason, it seems my Package Explorer is showing the folder structure of my project instead of its package structure. How would I go about "fixing" this? I've tried playing with the filters but it seemed of no avail.
Do you configure the corresponding folders to be the source folder?
They should be included in the java build path (The project properties--> java build path --> source ) . Eclipse only shows the package structure and provides the necessary stuff such as refactoring capabilities , checking java syntax error for the folders that are included in the java build path.