so my computer is new (i just built it) and i have the Asus M5A97 motherboard and it always boots into BIOS after it has been off. My boot order is fine but i was just wondering if what sata port my ssd was in (which has my windows 8.1 on it) would make a difference if i had it in port 1 or port 5. So would it matter if i had my other hard drives in sata ports 1-3 and then my ssd in port 5? Or am i being stupid and have no idea what im talking about?????
Without looking at your motherboard manual, I'm not exactly sure of this, but I'll give it a shot.
Good rule of thumb is to have your boot drive connected to the first SATA port (whether that's 0 or 1 depends on the naming convention of your board), then the rest of the devices come after.
Now as for using port 5, because I don't know the exact particulars of your motherboard, I am just guessing. Most motherboards that add additional SATA ports that aren't native to the chipset are put at the end. Meaning if your chipset supports 4 native SATA ports starting at number 1, then 5 and 6 are the third party SATA controllers. Third party SATA controllers are rarely as fast as the ones native to your chipset. They also are more trouble prone if you try to put your boot drive on them.
So I would keep you SSD which is your boot device on port 1, then use the next SATA ports for your HDD's. Only use your third party controllers if you have to. In my case I don't need them, so I disable them in the BIOS and therefore I don't have to install drivers for them in Windows.