As long as you’re using an xinput controller (Xbox 360/One/Series) the game will recognize your controller. There’s an option in the menu to prioritize controller over keyboard, which will make the game auto assign a connected controller to player 1. If you don’t have this toggled, you can press start any time with a connected controller, and a prompt will appear allowing you to press left to assign to player 1, or right for player 2.
If your controller is not an xinput device, there are a number of third party programs that will read any controller as an xinput device