Then, in Dolphin, select the "GCPad" option and select your controller on the left drop down menu, then select the "X360_controller_Dolphin" option on the right drop down menu (if the X360_controller_Dolphin option doesn't appear, try restarting Dolphin and verify that you copied the file in the correct location. ini file in C:\ Users\ Your user name\ Documents\ Dolphin Emulator\ Config\ Profiles\ GCPad. If you don't want to bother with that, you can use my config file here. In order to do that, you'll have to configure your Xbox 360 controller with Dolphin.
Your ISO file should now be added to your game list on Dolphin. Browse to the folder containing your MKW iso and click "OK".