Based on the different versions I've encountered, there seems to be several different approaches for configuring a gamepad to use on Citra, depending on which version is in use. I can't exactly point out which of these to use, best I can say is to give them a go and I assume 1 of it will run on yours. I had used a Logitec gamepad to test.
Method 1:
This one was re-copied from page 1 (1st post). This one need to be copy pasted to the "qt-config.ini" found in the Citra folder depending on where you had extracted it. e.g. [D:\citrafolder\nightlybuild\user\config\]
[Controls]
button_a="engine:sdl,joystick:0,button:0"
button_b="engine:sdl,joystick:0,button:1"
button_x="engine:sdl,joystick:0,button:2"
button_y="engine:sdl,joystick:0,button:3"
button_up="direction:up,hat:0,engine:sdl,joystick:0"
button_down="direction:down,hat:0,engine:sdl,joystick:0"
button_left="direction:left,hat:0,engine:sdl,joystick:0"
button_right="direction:right,hat:0,engine:sdl,joystick:0"
button_l="engine:sdl,joystick:0,button:4"
button_r="engine:sdl,joystick:0,button:5"
button_start="engine:sdl,joystick:0,button:7"
button_select="engine:sdl,joystick:0,button:6"
button_zl="code:49,engine:keyboard"
button_zr="code:50,engine:keyboard"
button_home="code:66,engine:keyboard"
circle_pad="joystick:0,axis_x:0,axis_y:1,engine:sdl"
c_stick="joystick:0,axis_x:3,axis_y:4,engine:sdl"
motion_device="engine:motion_emu,update_period:100,sensitivity:0.01"
touch_device=engine:emu_window
* Side note, e.g. button_a="engine:sdl,joystick:0,button:1" ; the number I colored red can be reassign to other button depending on how your gamepad layout is. Since it might differ from 1 brand to the next. My Logitec layout is (clockwise) Y-B-A-X, other might be X-A-B-Y, or maybe even Y-A-B-X. As such, make that code adjustment to your needs, or disassemble your gamepad buttons to the layout of your preference - whichever you find more convenient.
Method 2:
Similar to Method 1, this is another version of the setup;
[Controls]
pad_a=SDL/0/Gamepad/0
pad_b=SDL/0/Gamepad/1
pad_x=SDL/0/Gamepad/2
pad_y=SDL/0/Gamepad/3
pad_l=SDL/0/Gamepad/4
pad_r=SDL/0/Gamepad/5
pad_zl=Qt/0/Keyboard/49
pad_zr=Qt/0/Keyboard/50
pad_start=SDL/0/Gamepad/6
pad_select=SDL/0/Gamepad/7
pad_home=SDL/0/Gamepad/14
pad_dup=SDL/0/Gamepad/8
pad_ddown=SDL/0/Gamepad/9
pad_dleft=SDL/0/Gamepad/10
pad_dright=SDL/0/Gamepad/11
pad_cup=Qt/0/Keyboard/73
pad_cdown=Qt/0/Keyboard/75
pad_cleft=Qt/0/Keyboard/74
pad_cright=Qt/0/Keyboard/76
pad_circle_up=Qt/0/Keyboard/16777235
pad_circle_down=Qt/0/Keyboard/16777237
pad_circle_left=SDL/0/Gamepad/12
pad_circle_right=SDL/0/Gamepad/13
pad_circle_modifier=Qt/0/Keyboard/70
pad_circle_modifier_scale=0.40000000596046448
* Side note, e.g. pad_a=SDL/0/Gamepad/1 ; the number I colored red can be reassign to other button depending on how your gamepad layout is. Since it might differ from 1 brand to the next. My Logitec layout is (clockwise) Y-B-A-X, other might be X-A-B-Y, or maybe even Y-A-B-X. As such, make that code adjustment to your needs, or disassemble your gamepad buttons to the layout of your preference - whichever you find more convenient.
Method 3:
Similar to Method 1, another alternative to the setup;
[Controls]
button_a="joystick:0,button:0,engine:sdl"
button_b="joystick:0,button:1,engine:sdl"
button_x="joystick:0,button:2,engine:sdl"
button_y="joystick:0,button:3,engine:sdl"
button_up="hat:0,direction:up,joystick:0,engine:sdl"
button_down="hat:0,direction:down,joystick:0,engine:sdl"
button_left="hat:0,direction:left,joystick:0,engine:sdl"
button_right="hat:0,direction:right,joystick:0,engine:sdl"
button_l="joystick:0,button:4,engine:sdl"
button_r="joystick:0,button:5,engine:sdl"
button_start="joystick:0,button:7,engine:sdl"
button_select="joystick:0,button:6,engine:sdl"
button_zl="code:49,engine:keyboard"
button_zr="code:50,engine:keyboard"
button_home="code:66,engine:keyboard"
circle_pad="axis_x:0,joystick:0,engine:sdl,axis_y:1"
c_stick="axis_x:3,joystick:0,engine:sdl,axis_y:4"
* Side note, e.g. button_a="joystick:0,button:1,engine:sdl" ; the number I colored red can be reassign to other button depending on how your gamepad layout is. Since it might differ from 1 brand to the next. My Logitec layout is (clockwise) Y-B-A-X, other might be X-A-B-Y, or maybe even Y-A-B-X. As such, make that code adjustment to your needs, or disassemble your gamepad buttons to the layout of your preference - whichever you find more convenient.
Method 4:
Alternative pad config in case the first method fail to enable using your gamepad. This one need to be copy pasted to the "qt-config.ini" found in your directory [C:\Users\yourpcname\AppData\Roaming\Citra\config]
[Controls]
button_a="engine:sdl,joystick:0,button:0"
button_b="engine:sdl,joystick:0,button:1"
button_x="engine:sdl,joystick:0,button:2"
button_y="engine:sdl,joystick:0,button:3"
button_up="engine:sdl,joystick:0,hat:0,direction:up"
button_down="engine:sdl,joystick:0,hat:0,direction:down"
button_left="engine:sdl,joystick:0,hat:0,direction:left"
button_right="engine:sdl,joystick:0,hat:0,direction:right"
button_l="engine:sdl,joystick:0,button:4"
button_r="engine:sdl,joystick:0,button:5"
button_start="engine:sdl,joystick:0,button:7"
button_select="engine:sdl,joystick:0,button:6"
button_zl="engine:keyboard,code:49"
button_zr="engine:keyboard,code:50"
button_home="engine:keyboard,code:66"
circle_pad="axis_x:0,engine:sdl,joystick:0,axis_y:1"
c_stick="axis_x:3,engine:sdl,joystick:0,axis_y:4"
pad_a=65
pad_b=83
pad_x=90
pad_y=88
pad_l=81
pad_r=87
pad_zl=49
pad_zr=50
pad_start=77
pad_select=78
pad_home=66
pad_dup=84
pad_ddown=71
pad_dleft=70
pad_dright=72
pad_cup=73
pad_cdown=75
pad_cleft=74
pad_cright=76
pad_circle_up=16777235
pad_circle_down=16777237
pad_circle_left=16777234
pad_circle_right=16777236
pad_circle_modifier=68
pad_circle_modifier_scale=0.5
* Side note, e.g. button_a="engine:sdl,joystick:0,button:1"; the number I colored red can be reassign to other button depending on how your gamepad layout is. Since it might differ from 1 brand to the next. My Logitec layout is (clockwise) Y-B-A-X, other might be X-A-B-Y, or maybe even Y-A-B-X. As such, make that code adjustment to your needs, or disassemble your gamepad buttons to the layout of your preference - whichever you find more convenient.
One of these should probably resolve your issue with getting the gamepad recognized by the emulator. On a side note, if ever you accidentally press a button while opening the game controller setting from inside the emulator interface, and causes the gamepad to not work, simply re-copy paste the code which works.