If I understand your post title, it shouldn't be a problem to have the dirves set that way but your backup drive will only be able to backup half of your data. The RAID0 array will be 3TB and your backup will only be 1.5TB. If all the connections are SATA, you shouldn't have to set any jumpers, but you will have to enable RAID in bios for 2 of the three drives and then create the RAID array following the instructions in teh motherboard manual if you want it to be a boot disk, otherwise use the software in windows to create the array.
Another alternative would be to create a RAID5 array that would tolerate a single drive failure but you will still need a separate backup system to ensure your data is safe.
Hope that is of some help to you