Super edit: You can use steam's controller config and load the most popular config for this game. It maps your controller to keyboard commands and it appears to work extremely well. I've decided to recommend that above all else because my old Directinput controller has issues with win10.
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MBAA supports both Xinput and Directinput controllers, which is a problem for anyone using a PS3, PS4, or Switch pad because they all support that standard to varying degrees.
To make matters worse, when you emulate inputs the game either detects nothing or detects both your controller and the simulated input at once. I use a program called Xoutput alongside the ViGem framework and my Saitek pad would always be detected twice.
Below is what I posted in a thread on Switch pads, this may be helpful to you.

Ironically, I'd like to add that the game does in fact support directinput controllers, which is an issue because the game recognizes directinput from your ds3/ds4/switch controller as controller one and your emulated inputs as controller 2. There's a config file in system where you can swap the player1/player2 inputs to fix it.

This is the contents of the KeyConfig file in the SYSTEM folder which saves your control configs, I've noticed that P0, P1, P2, and P3 are devices identified in their connected order. This is important because it always seems to detect PC/ds3/ds4/switch directinput's first above all else, then the emulated Xinput from Steam/XOutput. What allows you to change the order of priority is P0_Num, P1_Num, P2_Num, and P3_Num. They take entries from 1 to 4, which is interesting because this game only supports two players, so what I've done in this entry is make my cyborg rumble pad controller number 3 and made the xbox pads (which steam emulates) 1 and 2.
Keep in mind renaming the controller entries does nothing, it will always show up as the first entry. I've also noticed that the game only writes to this file when you enter controller config, leave it, and then close the game. Hope it helps

[KeyConfig]
NoKeyboard= 0
P0_Num= 3
P0_Name=Cyborg Force Rumble Pad
P0_Val00= 24
P0_Val01= 23
P0_Val02= 22
P0_Val03= 21
P0_Val04= 10
P0_Val05= 0
P0_Val06= 2
P0_Val07= 3
P0_Val08= 1
P0_Val09= 4
P0_Val10= 0
P0_Val11= 6
P0_Val12= 0
P0_Val13= 0
P0_Val14= 2
P0_Val15= 3
P0_Val16= 17
P0_Val17= 18
P0_Val18= 19
P0_Val19= 20
P0_Val20= 0
P0_Val21= 0
P0_Val22= 0
P0_Val23= 0
P1_Num= 2
P1_Name=Controller (XBOX 360 For Windows)
P1_Val00= 24
P1_Val01= 23
P1_Val02= 22
P1_Val03= 21
P1_Val04= 10
P1_Val05= 0
P1_Val06= 2
P1_Val07= 3
P1_Val08= 1
P1_Val09= 4
P1_Val10= 0
P1_Val11= 6
P1_Val12= 0
P1_Val13= 0
P1_Val14= 2
P1_Val15= 3
P1_Val16= 17
P1_Val17= 18
P1_Val18= 19
P1_Val19= 20
P1_Val20= 0
P1_Val21= 0
P1_Val22= 0
P1_Val23= 0
P2_Num= 1
P2_Name=Controller (XBOX 360 For Windows)
P2_Val00= 0
P2_Val01= 0
P2_Val02= 0
P2_Val03= 0
P2_Val04= 0
P2_Val05= 0
P2_Val06= 0
P2_Val07= 0
P2_Val08= 0
P2_Val09= 0
P2_Val10= 0
P2_Val11= 0
P2_Val12= 0
P2_Val13= 0
P2_Val14= 0
P2_Val15= 0
P2_Val16= 0
P2_Val17= 0
P2_Val18= 0
P2_Val19= 0
P2_Val20= 0
P2_Val21= 0
P2_Val22= 0
P2_Val23= 0
P3_Num= 0
P3_Name=
P3_Val00= 0
P3_Val01= 0
P3_Val02= 0
P3_Val03= 0
P3_Val04= 0
P3_Val05= 0
P3_Val06= 0
P3_Val07= 0
P3_Val08= 0
P3_Val09= 0
P3_Val10= 0
P3_Val11= 0
P3_Val12= 0
P3_Val13= 0
P3_Val14= 0
P3_Val15= 0
P3_Val16= 0
P3_Val17= 0
P3_Val18= 0
P3_Val19= 0
P3_Val20= 0
P3_Val21= 0
P3_Val22= 0
P3_Val23= 0

I don't use steam's emulated input because it's spotty in my opinion, so if you have any advice on it PLEASE post it in the comments. The more info we can compile on this problem the easier it will be for players who are new to this.