It's 3GB per GPU. That's the number that counts, when considering if a given game will require more memory than you have, since what you actually have is two copies of the same data.
The memory usage indicator in MSI Afterburner, however, shows total memory usage across both GPU's, so you have to divide it in half to get the actual usage (i.e. what each single GPU is using).
In other words, nothing's wrong with your setup.