Basic Question: Is it better to concentrate HDD's on one controller or spread them out?

I have a NORCO RPC-4020 (20 hot-swappable drive bays) home server with over 11 (soon to be 13) HDD's in addition to a boot/OS SSD and DVD drive. The mobo has four SATA3 ports (two of which are used for the SSD and DVD drives), two PCIe and two PCI slots. I currently have two Supermicro AOC-SAT2-MV8 8-port SATA2 PCI-X controllers in the PCI slots, and have ordered a Syba SI-PEX40071 8-port SATA3 controller (and plan to get another if it works), after finding them refurbished for cheap. So, if all goes well, I'll have 2 free SATA3 connectors on the motherboard, another 16 SATA3 connectors on the PCIe controllers, and another 16 SATA2 connectors on the PCI controllers -- yes, complete overkill, but that's just the accidental way it turned out in terms of when I bought what.

As it happens, 7 of the HDD's are only SATA2, and the other 4 (soon to be 6) are SATA3.

I'm curious, should I put the 4 (soon to be 6) SATA3 HDD's on the same SATA3 PCIe controller, or should I spread them out between the two SATA3 PCIe controllers and the 2 free SATA3 ports on the motherboard?

This is a home media server, so the heaviest data traffic is when I am moving lots of big files between HDD's on the server, rather than watching movies over the network. Given that, the question becomes, are transfers faster between HDD's on the same controller, or spread them out so the controller doesn't "saturate"? Is there any reason to even use the SATA2 PCI controllers with the SATA2 HDD's, or should I put all the HDD's on PCIe cards, since PCIe 2.0 is so much faster than PCI?

Use HD Tune to determine how fast your drives are. Whether the drives themselves have SATA2 or SATA3 connections doesn't matter. Only today's fastest drives can utilize a full SATA2 connection, though we are on the cusp of that gradually going to change and they all come with connections fast enough to accommodate them, in this case SATA3. SSD's should always go on a SATA3 connection of course.

When planning out your setup factor the number of drives you have, their top speeds and your workload along with the type and number of lanes on the controller. Those Syba cards have two PCI-E 2.0 lanes for a top speed of 1000MBps. 4 very fast hard drives can max that out doing a transfer from 2 to 2 on the same controller, or in a RAID, or another software reading all at once. Just depends what you plan to do. If you are running a RAID you will definitely benefit from splitting them up or using controllers with 8 lanes. But if you are just transferring a few things here and there a couple drives at a time, it would be fine. What hard drives are you using and how fast are they?

Good quality PCI-E 8 lane cards can be had for cheap on ebay. Look at LSI and IBM.

CRAP! I just realized there's actually such a thing as a x2 slot -- I had assumed x1/x2 nomenclature were referring to the same thing, since Wikipedia has no mention of PCIe x2, only x1/x4/x8/x16 -- but now I find an article from 2011 saying Intel wants to create an x2 slot. And indeed, looking at the close-ups of photos of the SYBA card and my motherboard, the SYBA's x2 is too long for the x1 slot in my motherboard. Hopefully it will work with my x16 slot -- good thing I haven't bought a second SYBA card yet.

Yeah you can put it in your x16 slot no problem. Also keep in mind of course the scenarios I presented are best case just for guidelines. Most drives fall in between 100-200MBps and transfers aren't always going to be max throughput due to position on the drive and file size.

Well, I have read on forums people complaining that they tried putting the big x8 SAS cards in an E35M1-M Pro's x16 slot, it didn't work, and when they contacted support, they were told the x16 capability is only for video cards -- when the SYBA card arrives next week I guess I'll find out. The SYBA card was only $40 refurbished, so I figure I'll hang on to it for a future mobo setup even if it doesn't work with my current one.

OK, the SYBA 8-port worked fine in the x16 slot, but it didn't get along with the Supermicro 8-port PCI card -- the Supermicro BIOS doesn't load, and the card disappeared altogether in Windows Device Manager. Somebody in another thread mentioned they yanked the BIOS chip from their Supermicro 8-port in order to get it to boot when connected to an 8TB drive, so I was curious if yanking the chip would somehow fix my problem, so I yanked the BIOS and it worked! Then I added the second Supermicro card (after yanking the BIOS), but for some odd reason I can't get both Supermicro cards to be recognized by Windows at the same time -- if I remove one, it sees the other (and the drives attached to it) -- but it doesn't matter, because just one Supermicro card gives me 8 SATA2 ports to go with the 4 SATA3 ports in my old SYBA SI-PEX40064 and the 8 SATA3 ports in my new SI-PEX40071 -- for a total of 20 ports. Better yet, I discovered that not only do both PCIe cards use the same Marvell drivers, it turns out the latest drivers for the 8-port card also give 8TB support to the 4-port card (which previously didn't have drivers with 8TB support) -- so all 20 ports work with 8TB drives, and it looks like I'm all set.

Is there any real use for the BIOS chips on controller cards, if you're never going to boot from anything connected to them? Would the only effect of yanking the BIOS chips from my PCIe controllers be a faster bootup time, since the controllers would be removed from the bootup process?

I think you can setup hardware raid on those controllers and since they have a CPU, it does the work of the raid part and would need the bios, but not needed if you are only using the cards for its SATA ports. x2 slots are only 5gb rate so slower than the sata3 6gb speeds.. Lots of complaints from people about cheap marvel software. They are made for consumers for simple tasks and will break if used in a professional environment which costs 5-10 times as much. Usually it will start off like I used this or that at work and wanted the same thing at home but cant pay the thousands for those used at work and found this one but when I tried those exotic methods it broke.. They dont even implement all the stuff in hardware needed for such usage and kludge things so it appears to work.

Yeah, I'm not using RAID, which has major disadvantages when used with Seagate's SMR drives -- instead I'm using Stablebit Drivepool, which gives me a lot of flexibility in pooling various drives and choosing what to make redundant. So, yeah, all I need is a dumb controller to pass data between the HDD's and the motherboard.

Well adding 8 drives to a 5gb slot would mean thats the max transfer rate for all drives combined. Copying from one drive to another would be similar to doing it over USB. Unless they are on separate controllers.