If you go with making them on partitions, you may as well use RAID0 and get the full 4TB of space.
Each part of a RAID5 array needs to be on a separate physical disk - if you had 2 partitions on the same drive and that drive fails, you lose everything on the array.
If you are mostly concerned about storage space, and don't need full redundancy, you can use something like mhddfs (on linux) or windows drive extender on Windows home server. Those will make the drives appear to be a single drive, with all 4TB of space, but if a drive fails, you only lose what was on that drive. I do that on my home file server because it's mostly recorded TV and other files that I can replace easily.
If you want all your data to be able to survive a hard drive failure, create 1 partition on each drive and use those for the RAID5 array (or use the entire drives with a hardware raid controller). You lose a full drive worth of space, but you won't lose anything when a drive fails.
The reason for making a single partition is so that the drives don't appear to be empty to other operating systems and utilities - some will mess up a drive that looks like has no partitions.