I have decided to use two different sets of assets for desktop and android but I am not sure what the best way to do this would be? If anyone got some tip or suggestion on how to streamline this I would appreciate it!
I am using Eclipse and Gradle.
You can use two different assets folders. No one is forcing you to share assets for all platforms.
In build.gradle of Android project you can locate and modify assets.srcDirs = ['assets'] line. It stores a relative path to the assets folder. Since you want to keep separate assets for mobiles (or at least the Android version), I suggest you leave it as it is, though - just keep the android/assets folder as usual and store mobile assets there.
As for the desktop project, assets are referenced two times in build.gradle: in project.ext.assetsDir = new File("../android/assets"); and linkedResource name: 'assets', type: '2', location: 'PARENT-1-PROJECT_LOC/android/assets'. As you can see, they both store (sorta) relative paths that you can safely replace. Creating a new desktop/assets folder makes sense if you want to keep a similar folder structure. These two lines would be simply replaced with project.ext.assetsDir = new File("assets"); and linkedResource name: 'assets', type: '2', location: 'PARENT-1-PROJECT_LOC/desktop/assets' - and then you can just import the project as usual.
Note that this answer assumes that you generated your project with the default gdx-setup app. The default LibGDX project generator usually does not handle assets folder linking for you, so just remember to mark the new desktop/assets folder as resource in Eclipse.