So I recently purchased an MSI X299 Creator board and an Intel 9960x CPU. The board has three 8 pin CPU power connectors on it, and my EVGA 1300 G2 power supply only has two 8 pin CPU out puts. What are my options?

Could I do standard overclocking with the two 8 pins? Like 4.8-5GHz?

Thanks for all of your help. 

could supplying mobo with such high wattage shorten the lifespan of the cpu?

madoo
could supplying mobo with such high wattage shorten the lifespan of the cpu?

It's not clear just what you're asking.  But I think what you're implying is that a 1300W power supply is giving 1300W to the motherboard non-stop.  This is a common misconception.  Power supplies are on-demand devices, so the power supply will only provide what the motherboard/CPU/GPU demands of it based on power draw and current load levels.  1300W just stands for the maximum wattage to expect for the DC output going to the motherboard. 
 
On the flip side, if you're doing overclocking and increasing the voltage to the motherboard and processor, that will have an effect on the lifespan of the processor, but it's not directly related to the power supply when it is operating normally (if a PSU fails or is running out-of-spec, that's a completely different matter....).  There are a handful of voltages in your BIOS that are recommended not to increase over a certain amount, as those voltages can cause damage to the motherboard, memory, and/or CPU.  However, for reasonable overclocks, raising the voltage and overclocking will affect the lifespan of your CPU; it's just not clear exactly how much it affects the lifespan.  Could be a day, could be a year.