In general, those settings typically only need to be configured once since they are stored in non-volatile memory and should not need to be changed while your system is running. Because of this I would recommend configuring the settings for your Maestro with the Maestro Control Center beforehand.
That being said, it is possible to change those settings from a Linux script by invoking UscCmd, our command-line utility for the Maestro which comes with the Maestro Control Center. The "--configure" option of UscCmd allows you to change all of the settings of the Maestro, and you could look at the C# source code of UscCmd in the Pololu USB Software Development Kit to see how this is implemented if you are curious. However, please note that these values are stored in the Maestro's EEPROM, which is rated for 100,000 erase/write cycles, so you should be careful not to change them rapidly in your program or that limit could potentially reached quickly.