The extra 4-pin CPU power connector, labeled as "CPU_PWR2" is for supporting additional power (75W +12V) to the CPU if you OC your CPU. Plugging EPS2 power cable into CPU_PWR2 is optional and isn't needed for normal operations of MoBo.
Most PSUs have only one 4/8-pin power connector for CPU since most mainstream MoBos only have one 4/8-pin EPS2 connector for CPU power. Server MoBos (e.g X299 chipset) usually have 2x 4/8 EPS2 power connectors for CPU. With those MoBos, you also need to use high-end PSUs that come with multiple 4/8-pin power cables for CPU. E.g Seasonic PRIME 650 80+ Titanium which is powering my Skylake build (full specs with pics in my sig).