If it comes into the CAC at the top, the coolant will still fall down and flow through even if it's low. If it comes in the bottom, the flow will be aided by the rising of the coolant as it's heated. I have mine running in the bottom and out the top at the moment, but the other way is safer and I doubt the heating of the water adds much to the flow. The stock setup flows into the top and out the bottom of both the CAC and the CCHE.
I capped off the overflow line last week, and made sure it was full. Over the weekend, I checked it after it had been parked for a while and it was quite low. After driving it, I checked again and it actually ran over. Last night after sitting, it was quite low again. This leads me to believe that even though it doesn't get extremely hot, it does get hot enough to cause quite a bit of expansion and contraction. Because of this, you're quite likely to get air bubbles (especially if you haven't capped the overflow). Because of that, I'd say to play it safe and route it into the top of the CAC, until someone can prove that the rising heat adds a noticeable amount to the flow.