the controls are a complete mess in this game. Keyboard controls aren't labeled correctly, half of them are missing from the config screen, and the game hates controllers by default. Any help here is appreciated.

Dunno whats up with your game but mine were labeled correctly and they are all there, you just need to click the down arrow to see them all. I would probably default the keyboard controls. Then program it. I'm not at home to take screen but...

My setup is:

Left Joystick = Arrow Keys

X = A (Action)
A = Spacebar (jump)
B = D (Devour Soul)
Y = F (Aim/Shoot)

LT= C (crouch)
RT = S (Sneak/Target)

LB= Left Cntrl

Left on Right Joy Stick = Num 0
Right on Right Joy Stick = Right CTRL

Back = Enter (glyph menu)
Start = Esc (options menu/save menu)

What about when it says to use the numbers? They dont' do anything at all for me.

There not missing you got to scroll down in the settings,just highlight the up/down arrow and press enter or 2,square, or B depending on your controller to see the rest of the buttons.

Don't use the Gamepad Controls in-game while using Xpadder. Just leave it on keyboard controls and map the keys using Xpadder\.

The controls aren't really a mess, they just use DirectX and not XInput.

Turn of the gamepad (it will still work in menus though) reset your keyboard setup and setup Xpadder.

Or, if you don't really need to use Xpadder, I strongly suggest the superior (IMHO) Pinnacle Gamepad Profiler.
I made a profile for that in another thread.