I would recommend putting your refugium on the end of the tank if at all possible, flowing into the return section, so it looks like:
-----------------------------------> <-------------
Inlet | Skimmer | Baffles | Return Pump | Refugium
That way you can fine tune the flow going into the refugium (tee off from return flow if you have extra capacity), but also have a tall refugium and maximise water height as opposed to being restricted to being lower than the skimmer chamber height.
For nutrient export in your refugium, bigger is always better. With a small refugium you will get lower nutrient export, there is no real "ideal size", make it as big as you can and live with it.