You have your input and output arranged in almost the exact same way that I do. Although I had never thought about adding some more 90 degree holes ... I very much like that idea. Maybe I'll do that today!
Onto your question though, it really doesn't matter. I would leave an inch or two of free water around both the input and output, just to keep them free of plant leaves (input) and to avoid having the output batter any of your plants.
On the whole, it really doesn't matter that much, as you're still going to have plenty water cycling through your filtration system at any given time. Just keep a small area of clear water around each, and (at least in my experience) you'll have no problems.