Cortex M3 clock configuration
I'm not going to take the time to study an obsolete microcontroller but I will speculate based on my knowledge of NXP's Cortex-M3 processors.

The microcontroller has a crystal oscillator that can operate at some reasonable frequency, say 12MHz. The microcontroller also has an internal oscillator that is not as accurate as a crystal oscillator but uses an RC time constant to set the frequency. The processor core can actually run much faster than either of these oscillators, say 72MHz, so the chip provides a PLL that can be used to synthesize a higher frequency clock.

When configuring the microcontroller you can decide which of the oscillators you want to use: the crystal oscillator or the less accurate RC oscillator. I'm guessing that the SYSCTL_OSC_MAIN configuration bit performs that selection.

You can also decide whether to operate the processor directly from the selected oscillator or use the PLL to increase the frequency. My guess is that SYSCTL_USE_PLL selects the PLL as the system clock source. If you do use the PLL then there may be other parameters that are needed, such as indicating the approximate value of the oscillator frequency with SYSCTL_XTAL_16MHZ.