External Sata vs internal sata

Hello, I have a question regarding external vs internal SATA ports. I'm building an I5 750 rig with an ASUS P7P55D Pro mb. The mb has one SATA-E1 connector (black) and six SATA connectors (blue). Is there a difference? The mb came with a external SATA port kit. The NZXT Tempest case also has an external SATA port. Leaving me the option of two external SATA ports. Bottom line, can I use one of the "blue" ports as an external SATA connection?
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More about external sata internal sata
  1. The black SATA connector is controlled by the JMicron JMB363. The blue connectors are controlled by the P55 chipset. A blue connector can be used as an external SATA port, but for hot-plug functionality, you need to set the SATA controller into AHCI or RAID mode. The JMicron drivers (get them from JMicron) enable hot-plug functionality.
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