According to the specs, you only have one HDMI slot available. The reason is because you have a discrete graphics card installed - AMD Radeon R9 390X. Built into the card are 2-DVI ports, 1-display port and 1-HDMI port.
The 2 other HDMI ports are wired into the motherboard and will only utilize the intergrated graphics of the i5 CPU.
If a discrete video card is installed, the intergrated graphics are disabled. They cannot run simultaneously.
The best way to get a 2nd HDMI port is to use an adapter for one of the DVI ports on the AMD card to convert to HDMI.
They are very inexpensive online.
NOTE: a DVI to HDMI adapter will only provide Video signal, not audio.