Is there someway to make the changes from the GPIO utility permanent? Right now if I restart my RPi the changes revert back. I know I can use a script, but is there someway I can make the script start immediately at boot up since I'm using the GPIO to control motors and I don't want them to go crazy (100%) on bootup.
It is possible (but far from simple) https://www.raspberrypi.org/documentation/configuration/pin-configuration.md
No, there is no way to guarantee the state of the GPIOs between power-up and the time your software runs (likely to be at least 20 seconds or so).
You will have to use external hardware to drive the GPIOs high or low if you want to control the GPIO state during that period.
You could use a tri-state buffer between the GPIO pins and your motor controller. Use a one-shot on the enable pin(s) to delay turn-on for long enough to complete the boot process. Resistors (~10K) on the output of the buffer can be used to set the initial state.