Motherboard RAID solutions are somewhere between software RAID (OS supported) and hardware RAID. There's some "intelligence" built in, but it's not the same as hardware RAID.
I'd suggest a quick read here http://en.wikipedia.org/wiki/RAID#Implementations
This might also be a good resource http://www.storagereview.com/guide/ctrl.html
A lot of people seem to refer to the motherboard implementations as FakeRAID, although it's not as such, it's just not the same as a high-end RAID card.
The main difference is that a high-end solution has an onboard CPU that offloads the system and there's generally a fairly generous amount of cache memory on proper RAID solutions.
RAID 1 should be perfectly safe to run off the motherboard controller, as it just writes the same data to both drives. However, something a bit more exotic like RAID 5 might not give you the performance and safety that you'd expect.
There's a reason why "real" RAID controllers cost as much as they do. They're generally not intended for consumer PCs and thus cost a fair bit of extra money.
Just be glad that you started using RAID now and not a few years ago, as the so called RAID solutions back then weren't nearly as good as they are now.
Reading your post about your setup, it seems like your switch from RAID to AHCI might have cause a bit of an issue as you can't just go changing modes in the BIOS and hope for the best. There's a reason as to why there are different operational modes, but then again, the implementation isn't exactly great, just for the reason you explained that if you have drives connected that aren't part of the RAID array, you'll end having strange problems. You might want to take a look here as well for some of the issues that may happen in a RAID setup http://en.wikipedia.org/wiki/RAID#Problems_with_RAID
Also, RAID doesn't guarantee that you're protected from hard drive failures, these things sadly happen. I haven't had one go down for three years (knock on wood), but I had one fail with the replacement for that one fail within two weeks, that wasn't much fun.
Still, for your needs I'd invest in a real hardware RAID controller, as it'll not only offer vastly improved performance, but it should also offer a more solid RAID solution. Apart from Adaptec, 3Ware
offers some high-end solutions and even Intel
has some dedicated RAID controllers.
If I where you, I'd be running RAID 5 rather than RAID 10, it's a much better solution to keep your data safe. Good luck finding a suitable solution for your needs.