Gamecube emulator

What is a good one, and how do I use it???

http://www.emulator-zone.com/doc.php/gamecube/dolphin.html

Mk, now, how do I regester my USB controller with it?

Go to the main site to download different version of this emulator,
and check the game compatibility.
http://www.dolphin-emu.com/As for the controller,
connect your USB controller, go to Options -> Configure,
Go to 'Plugins' tab, under the 'Pad' menu,
Choose nJoy, then press 'Config' button next to it.Then, Configure your controller button.

Why can't they all be as simple as project 64 T.T

Because it is a Dolphin, not Project 64.Most of today emulator is still new, and haven't reach the final version yet.
Maybe the final version will be more easy to navigate, or friendly user.