I just finished a box, and I went with the small hole and pulled the wires through. There were a couple reasons why I chose this route. I did not have a terminal cup available (could have took it off another box, but decided not to). Also, I feel that there is a better chance for air leaks with the terminals..won't be as significant with a ported box, but I would definitely want to make sure I have no leaks for a sealed box. Also, I prefer one run from the speaker straight to the amp since I was running more power to my new setup. I just drilled it small enough to force the wire through and silicone the gaps on the inside and outside of the box. Only con's I see with this method is that it does not look as presentable/good as the heavy duty terminal cups.
You might want to take a look at another option such as the binding post..a mix of both worlds. It looks nice and I believe that it won't be as prone to leaks as terminal cups