For the 2 x 1000GB drives, is it possible that the RAID software is assuming a RAID 0 (span) set and so describing both disks as part of that array? RAID 0 would certainly give you 1000GB, and it may just be a "brain dead" GUI issue in the way it describes this to the user. Perhaps it is just offering you that as a default config and you are expected to override this with a RAID 5 config if you want that across 3 disks. As for the degraded/rebuilding state goku is right - this is normal when you first set up a RAID array and even in hardware RAID will often take several hours for large disks - it is just building the stripes and setting up the parity blocks. Perhaps backing up in the GUI is confusing matters. Can you just confirm the config and then periodically monitor the status over several hours? Or does that come up as "failed" as well?
If you have a "hardware" RAID option it would be worthwhile checking with the hardware/BIOS manufacturer whether this works under Linux. You need to know if it is a system driver running under an OS or whether it runs at a lower level. One way of determining this could be to find out whether it supports providing RAID for the boot system disk (any OS) - if it does then this would imply that it isn't a system driver but implemented at a lower level, in which case it doesn't matter whether it is a real RAID controller or just software masquerading, you should be able to set up a "hardware" RAID container in the BIOS, and this will simply present to Linux as an ordinary (1TB) LUN - Linux should not be capable of distinguishing between it and a normal drive which will make things easier for you and you won't have to work out what is wrong with the Linux software RAID system. Its also safer as you are not dependant on Linux to manage the RAID set, and probably faster, too.
BTW - I assume that you want RAID 5 for redundancy rather than speed? If you are more looking for speed then RAID 5 is not the right choice as this is slower than simple single disks in most operations.