To see / set up the build-time classpath for your project, select the project, open the pop-up menu, choose Properties and go to Java Build Path.
By default, the run-time classpath for projects is the same as the build-time classpath. You can change it by editing a Launch Configuration (Select Run > Run from the menu bar).
By default, the Java builder copies all resources from your project to the build output folder (typically called bin). You can exclude some resources and resource types by setting your preference in Window > Preferences > Compiler > Other.
You can put your files on the classpath without placing them in a source folder:
Put them in a class folder by using Java Build Path > Libraries > Advanced on the project's Properties
Alternatively, you can put them in a JAR and add the JAR to the classpath.