Storing the new configuration (baud rate or update rate) in RAM means the GPS module will revert to the default configuration when it is reset or powered off.
Storing the new configuration in FLASH means that it is permanent. The next time the GPS resets/powers on, it will load its configuration from the non-volatile FLASH memory. In your case, it would start running at the faster baud rate and update rate.
Some people store the configuration in FLASH so they can run it once, and then remove the configuration commands from the sketch. You can also use a utility to configure the GPS permanently (i.e., in FLASH). I've never been a fan of that, because it requires the same extra steps for anyone else using your sketch. If you replace the GPS module, it would have to be reconfigured. Just leave the configuration commands in your sketch, unless you really need the program space. It's probably less than 100 bytes.
Cheers,
/dev