Does this controller operate with using the brake light coming on to then put power out to the trailer brakes? if so you might mount the control bax in the trunk and then find one brake light wire in the trunk and splice into that. and then run the wires back out to the hitch unit. being you did not tell the model of the controller it will be a bit harder to help. but the controller i have hooked up all used the brake light power to start powering up the trailer brakes.

if by chance you have one that also has the lever on it so you can do the brakes separately then that need to be by you. so send the model of the brake controller so we can look that up and help you better.
here are some links to different controller that may help you out.

https://ricardolevinsmorales.com/tekonsha-brake-controller-wiring-diagram

https://ricardolevinsmorales.com/tekonsha-brake-controller-wiring-diagram

https://ricardolevinsmorales.com/prodigy-brake-controller-wiring-diagram

here are some youtubes
https://ricardolevinsmorales.com/prodigy-brake-controller-wiring-diagram/

once you get to the yutubes they have a lot of them to show you different ways to do this.
good luck

Didn't it come with a wiring diagram? If you don't have a wiring diagram for your vehicle, don't do this yourself. You can really screw up things under the dash if you don't know what you're doing.