Ok, i am by no means an expert and personally haven't rom'd my phone. My brother has tho.
Im assuming you're using safestrap? What seems to be an issue is some sort of partitioning. From what I've seen in my brother's s4, safestrap allows you X amount of slots. The first slot is always taken up with your original rom. So it SEEMS in essence that it's basically adding a rom(hyperdrive in this instance) to everything else that is still currently on the phone. That's why you're running out of room. My brother has the same problem and this is the main reason i haven't even bothered with it.
As i said, im not as savy as some of these guys here, but i believe that's the long and short of it.