The answer depends on what you are using the server for, and why you need redundancy. If you are storing critical data on the server, and thus you have to have data redundancy, that is one thing. On the other hand, if you also need your server to be running 24/7, and can't let it go down, then that is another type of redundancy.
If you are in the first situation, then the answer you proposed will work fine: you should put all your data on a RAID 1 between the two SSDs, and run your OS off of the other SSD. This actually isn't as risky as it sounds, because the OS is not critical to your data; if the single drive dies, all you have to do is get a new drive, reinstall the OS, and you are back up and running.
However, if you have to have your server running 24/7, the above solution is not good, because it will cause the server to be down for up to a few days while you get the OS installed. Therefore, for this scenario, I would suggest putting both the OS and the data on the RAID 1 between the SSDs, and leaving the other SSD for making backup copies of important files, or whatever you want. This arrangement will be slightly slower than above solution, but will ensure that the OS doesn't ever go down.
Just as a side note, the specific OS that you use has absolutely nothing to do with the RAID configuration of the server, as long as you are using hardware RAID. (I am assuming you are.) You can use Ubuntu Server or Windows Vista, the server doesn't care. I am also assuming that hardware restrictions keep you from putting all three SSDs in a RAID together, because if they don't then the obvious solution is to put all three drives in a single RAID 1 and put everything on there.
--EDIT--
Apparently I assumed wrong; as you posted below you are actually using software RAID, which changes everything. Because you are running the RAID controller from inside the OS, if your OS goes down, then you loose all your data. Therefore, it is dangerous to put your OS on a single drive without redundancy. Also, software RAID is dependant on the OS, so it actually does matter what OS you use. Windows is able to run software RAID on the boot disk, but as far as I can tell, linux is not.
Because you don't want to loose space by doing a three-disk RAID 1, at this point the best option is to do a RAID 1 with the two bigger disks and put all your data and OS on that. You will have to run some version of Windows and use their RAID software to set it up. I don't know what you should do with the other disk, because it is impossible to have redundancy with a single disk, so it is pretty much useless.
I hope this helps!