If you are using that 3TB disk on a 64 bit system (OS and hardware) installing any operating system should be straight forward.
Installing and using your disk with a 32 bit system can be troublesome.
If you are installing your 3TB hard drive on a system that is 32 bit and not 64 bit you will get in trouble with anything bigger than about 2.2TB since you can not address more than that.
(2^32) * 512 is the maximum where 2 is for binary, 32 is the number of bits your system can address and 512 being the sector size (bits per sector). I have seen newer hard drives having bigger sectors, in which case you can install larger disks than 2.2TB.
The documentation you refer to says 64 bit, so if you make sure that you install a 64 bit operating system as well, this should be pretty straight forward.
If you choose to install Debian, then partitioning your hard drive will be the one of the "hardest" parts of the installation. If you're going to run this machine in a production environment you can tell Debian to partition your set up automatically and then do changes that fit your needs.
I have not installed the Ubuntu server edition in a while but I suspect, since Ubuntu is a derivative of Debian, the installation process will be is pretty similar.
Hope this helps.