When I use 2 controllers (that are the same), it seems to happily detect both with just the first set of lines. i.e.

input_device = “USB Gamepad ”
input_driver = “udev”
input_b_btn = “2”
input_y_btn = “3”
input_select_btn = “8”
input_start_btn = “9”
input_up_axis = “-1″
input_down_axis = “+1″
input_left_axis = “-0″
input_right_axis = “+0″
input_a_btn = “1”
input_x_btn = “0”
input_l_btn = “4”
input_r_btn = “5”

When you start a rom it should have some yellow text at the bottom of the screen confirming detection of the controllers.

If you wanted to specify both controllers, I’d disable the autoconfig and just manually add the lines to the retroarch.cfg

This may help a bit: