I recently bought an ASUS P7P55D motherboard to build a new system with, and I had a question regarding which SATA connector I should plug my HDD into. In the motherboard's manual it seems to list 2 types of connectors - 1 which is labeled JMicron JMB363 SATA connector (7-pin SATA_E1), and 6 which are labeled as P55 SATA connectors (7-pin SATA1-6). I am very much a novice builder and I'm not familiar with what the difference is between these two types of connection, so I'm not sure where to plug in my HDD. I only plan on using one HDD, and my optical drive is legacy and will need to be connected via PATA. Can anyone offer some advice on what the difference is between the two options, as well as which I should be using?
You could use either but I recommend you use one of the SATA connectors from the P55 chipset (SATA1 to SATA6).
SATA ports 1 to 6 are controlled by the Intel P55 chipset. The JMicron controller chip handles any PATA devices as well as the external SATA (eSATA) port on the back of the motherboard. I believe SATA_E1 simply gives you one more port.
I recommend using the Intel P55 chipset ports primarily because of driver availability and updates.