SATA puzzle on MSI P965 NEO-F

My MSI P965 NEO-F motherboard has 5 SATAII connectors, numbered 1 3 4 6 7. I had the PC assembled for me and find that my SATA HDD is connected to the second connector (3). When I asked the technician at the shop he just shrugged his shoulders and said it didn't matter.

Those 5 connectors are all identical, arranged on the board like this:
SATA1
SATA3 SATA4
SATA6 SATA7

Under Specifications, I find additionally:
- 4 SATA II ports by ICH8
- 1 SATA II port by JMicron JMB361
- Supports 5 SATA II devices

The latest downloadable manual shows that SATA1 is the JMB361 port.

I am puzzled by the curious numbering of the connectors and by an apparent anomaly in the BIOS (identical in the manual), which has the following list:

IDE Primary Master: NONE.
IDE Primary Slave: NONE.
IDE Secondary Master: My HDD.
IDE Secondary Slave: NONE.
IDE Third Master: NONE.
IDE Fourth Master: NONE.

How could 5 connectors serve 6 HDDs?
Should my HDD not be connected to the first connector?

I am thinking of installing a second HDD for backup purposes instead of a USB disk and would like to know where to connect it - and to know whether my HDD should not be connected to SATA1.

Gwynne

 

A Puzzle indeed

Actually you can have seven hard drives.
The JMicron PATA can have a primary and secondary drive on the IDE cable. There is one SATA on the JMicron. There are 4 SATA on the ICH8. That's a total of seven IDE drives: 2 PATA and 5 SATA. But we are still left with how those map to the six shown on the BIOS "Standard CMOS Features" screen: Primary Master/Slave, Secondary Master/Slave, Third Master and Fourth Master. I know from experience that board socket SATA3 maps to IDE Secondary Master. But, without running a bunch of experiments, it isn't clear how the rest map or where the 7th one is.
The other thing that would be nice to understand is how the drives map into winxp device manager where I see 3 primary controllers and 3 secondary controllers which could be 12 devices!!!