my old Asus motherboard actually had two different raid controllers but even so I wouldn't be afraid to run two different arrays on one board... I plan on doing it in my system I have now. Depends on wether or not your board will support it. Also another monkey wrench is that most (maybe not all) raid conrollers are PCI based which can only handle Sata 1 due to bandwith restrictions. I haven't checked if they make PCI-X cards or not.
My Gigabyte MB has 2 RAID options. The GigaRAID with 2 drives in either 0 or 1 and the Intel Matrix RAID on the ICH 10R Southbridge.
I run XP on my GigaRAID in RAID 0 and I run Windows 7 on my Matrix controller with the 2 drives in a RAID 0+1 configuration.
The Matrix option allows for more than one RAID array to be run ........RAID 0 , RAID 1 , Raid 0+1 ,RAID 5 or even RAID 10 and pretty much any combination of those you would want.
For the RAID1 (mirror) the motherboard RAID is probably fine as most of them will still let you pull a single drive and access the data. The motherboard will probably perform just fine as it's only mirroring.
For the RAID0 (striping) I would go with an external RAID card. The external RAID card (especially one that has the ability to do it's own computations rather than the systems CPU) will perform better and should you have to move the array to another system, you can move the RAID adapter with it (motherboard RAID1 may very well not be compatible form one mobo to another so no migration available).
I would never consider doing a stripe set (RAID1 or RAID5) using onboard controllers.
You should not be using raid for performance reasons, especially if you are going through the expence of buying an seperate controller. That money is better spent on and SSD for gaming and OS load times. Good raid cards that do hardware RAID are expensive. Load times with a RAID 0 are better by only a small percentage, but SSD load times are noticeably faster. You can boot and games off the SSD and then use the integrated RAID controller (the free one ) for RAID 1. Better still is no raid and an offline backup of your data that is not connected to your computer unless the backup is taking place.