You can play using two gamepads, yes. There is a tab in GFCE UltraX (recommended over FCE Ultra) called "Input" where you can map the buttons to the buttons on the pad. A on one controller will not register as A on the other controller. GFCE UltraX (gfeux) can be installed in Ubuntu by running
sudo apt-get install gfeux in a terminal, or simply clicking this link (doesn't work in Chrome).
As for the controller, I don't know if it works well in Ubuntu or not (most do), but it seems quite expensive for what it does. If you're open for suggestions, I'd recommend taking a look at a Saitek P380. It costs a fraction as much, has two analog sticks, an omnidirectional d-pad, 4 regular buttons + 4 shoulder buttons and start and select buttons. I have one and it works perfectly in Ubuntu.