Step 19: Upload your measurements to the machine
You need to upload it by going on the setup tab, you might already be there, and clickking Upload machine spec. This saves the new size into EEPROM on the arduino, so it'll stay there even when the power is lost. Unless you change the sizes, this is the only time you have to do that. Page size isn't relevant here, only machine size.
If you're curious (and why wouldn't you be?) Download machine spec does the opposite - it set's the machine size in the controller to be whatever the hardware has saved. This might be useful if you delete your configuration file sizes and don't want to measure it all again.
But remember that the configuration file doesn't ever get updated until you click save properties. So remember that if you make changes you want to keep.