It ultimately depends on the implementation of the RAID that's built into your motherboard but often times this "hardware" RAID is little more than software RAID facilitated through some proprietary drivers that will need to be loaded into the OS.
If this is the case, IMO, it's almost always better to use the stock software RAID that's included with any Linux distro. I've used the
mdadm software RAID + tools for over a decade and have never had any issues with it. The performance is solid and there are extensive tutorials and guides available on the internet to walk you through the various task such as setting it up, growing it, shrinking it, add/removing HDDs, etc.
This guide titled: 10 Surprising Facts About RAID also agreed with this position.
2. Software RAID is almost always a better choice than hardware RAID
Software RAID has advanced significantly in the last few years (as of 2012). Hardware RAID still has the three key vulnerabilities it has always had: First, it is expensive. Second, if your RAID card fails, your RAID volume fails; it is a single point of failure. Third, if your RAID card fails, you must find an exact replacement for that card to recover your data.
On the other hand, software RAID costs nothing, and if your controller card or motherboard fail, you can just move your disks to another machine and set up the appropriate software to read them.
3. Some “RAID cards” aren’t hardware RAID
Over the last few years SATA disk controller cards and motherboards have come out that claim to offer hardware RAID. They are really just disk controllers with BIOS that implements RAID in software.
How can you detect these cards and motherboards? Usually price is the giveaway. A $20.00 card is not likely to implement true hardware RAID. Also these cards usually offer windows-only support. Here’s a good writeup.