uEnv.txt, GPIOs, and overlays

I am using a beaglebone black with a custom real-time linux OS made with yocto to interface with CAN and some other things.
My custom cape uses the CAN pins on P9 and also needs to use some of the GPIO pins on P8.
I got the CAN working by simply including the can0 and can1 pinmux and peripheral .dtsi files to my dts and compiling, but no matter what I try, I can’t set the GPIO pins to 0x27 (Pulldown, input, mode7)
While trying to create an overlay or modifying the dts or it’s included files, and in previous stages of development, I found that i don’t have a uEnv.txt file and when I created one from examples online it didn’t seem to change the parameters I tried to change.
I am using version 5.0.x of Robert Nelson’s dtb-rebuilder for my dts files and yocto 2.7.1.

If anyone could either tell me how to fix uEnv.txt and/or how to make and implement an overlay correctly that would be very helpful.

Please let me know if you need any more information about my setup/files that I am using.

Thank you in advance,