Bundle (put next to the bundle) resources get included next to the binary of your game. They are useful when you want something included with your project but also easy to edit. An example of a custom resource which you could use is putting your game’s localization files there instead of inside of the bundle, that way, assuming you have the glyphs enabled, anyone can translate your game. Another example of something you would want to include as a custom resource are FMOD audio banks, including them in bundle resources makes them take up more memory and be less efficient.
Custom resources get bundled inside of your game’s asset bundle. They are not easy to edit (or at least that used to be true). Generally if you don’t have a reason to have a custom asset be external you want it internal.
Normal assets, as in ones Defold knows about and are linked internally in your project, are automatically included in the bundle.