As far as is goes with setting up the card or the software RAID it is basically the same. the only difference is the Controller uses it's own resources to control the RAID where the software uses the systems resources.
my suggestion is go with the onboard RAID, it will be the easiest for you. The bigger question is what type of RAID do you want to use?
Is "onboard RAID" the same thing as "hardware RAID," ie - PCI RAID Card?
RAID 0 for the 3 Internal Drives, and (for the time being) RAID 0 for the External backing them up. (again only until I can double the capacity of the external to allow for a mirrored RAID instead.)
I guess I could just save myself the hassle and go with two sets of external RAIDS (one for work, and one for backup) but I've heard that having an Internal work RAID gives you better performance. Any truth? Any card suggestions?
The only drives you want to be RAID0 are your OS/boot drive, your swap file (with enough RAM, you don't need a swap), and if you have your programs installed on a different drive. You would probably want 2 x 120GB SSDs. Then you have a 2nd array running 4 drives in RAID10 that stores all of your data and an image of your RAID0 array.
And thats how you get ants!
Have you seen issues with certain HDD's and RAID cards? The last system I built with nvRAID and Western Digital Black isn't 100% perfect. The SATA drives (even the Black ones) have some longer timeouts than the RAID, and cause the system to either 1) report an error or even better 2) BSOD (occaisonally). I did notice WD did pull the TLER utility from the webz.