If the overflow box siphon is broken,(which it shouldn't if it is designed correctly) your sump will not fill it will empty. It will overflow the main tank. But, It is good to leave yourself a little room anyway.
I don't think it matters where you place the skimmer, although it is nice to not see it by hiding it in the sump. The water entering it is the same. I have noticed a little more production out of my SEA clone however since putting it in the sump. I believe this is because the distance the water travels in the pipe is shorter, but it doesn't make that much of a difference. I probably just adjusted it better.