after doing more research it seems you have to compile the dts files into a pre processed file with cpp command before you can compile into a dtb file with the dtc command. so i got that figured out and can change the io pullups.
however im still struggling with the wakeup from suspend conditions. I enabled several of them but none seem to work. usb hubs are suspended so usb wakeup doesnt work, the Uart0 wakeup condition is enabled but doesnt wakeup the processor either. ill have to keep digging, but if you are anyone knows how to wakeup from a source other than the power button that would be great to know. as it stands ill have to add a secondary microprocessor to the system to ground the power button contact physically to wake up the board.