I might add that I had trouble configure controllers on the Dolphin core before moving to external disk. So what I did before moving to ext disk was to try updating Dolphin core to see if it helped with the controllers (which it didnt). It did however download a different Dolphin core, which after a lot of experimenting I got to configure the controlls succesfully. So I kept the setup with two Dolphin cores installed.
First core was named Dolphin 0.1 I think and the second active one has a name with Dolphin-emu and some numbers behind.