Onboard vs PCI-E 1x RAID Controller

Is there any speed difference between Onboard and PCI-E 1x RAID Controllers? I got a PCI-E 1x RAID controller to do RAID 0, but I didn't realize my mobo supported RAID. Wouldn't PCI-E become a bottleneck since it has a cap of 2.5 Gb/s while the SATA II HDs have a cap of 3 Gb/s for each drive? And is the mobo RAID controller software or hardware based?

Don't tell me to not use RAID 0 please.

Maybe not for you, OP, but for others. Although SATA II has a max burst speed of 3Gb/s, you'll never see that on any sustained basis. Likewise, you'll never see 2.5 Gb/s sustained through a PCIe x1 bus, either. So the PCIe x1-mounted controller is not going to create a bottleneck. Done properly, it can actually speed things up a little, and provide some protection against future failures.

ALL RAID controllers "built in" on the mobo's Southbridge use "software RAID". That is, it has all the code required in the chip, but most of the actual processing is done by the CPU. If you install a separate RAID controller card, especially the cheaper ones, you may get the same result - the card has the HDD controllers and code, but no dedicated processor on board, so it assigns all processing to the main CPU. But better-quality cards have their own processor on board and do all the work themselves, freeing up CPU time. That's how you MAY get a small performance boost from using a separate card.

One thing that worries users of RAID arrays is how to recover from equipment failure. This has it roots in the fact that there is no universal standard for the low-level details of how RAID disks are written and managed. The result is that RAID disks written by one controller system probably will NOT be usable by a different manufacturer's controller. The best protection for the entire RAID system, like any other data storage system, is an excellent data backup system with frequent redundant backups stored offsite, etc. But to protect against failure of the controller itself, one option is to use a separate dedicated controller card (rather than built-in on the mobo) from a major manufacturer, in the faith that the card can always be replaced by a new one from the same manufacturer that is guaranteed to work with drives already written by an earlier card.