It's not a huge deal, but since you're starting from scratch I would do
Filter Socks > Refugium > Skimmer > Return.
Refugium's work better when placed in front of the Skimmer, or even Parallel to the Skimmer because a lot of the nutrients that the refugium uses to grow would be "skimmed" out if the skimmer was placed in front. Obviously the skimmer won't skim out everything, but if we're going with best practice, try and feed the refugium as much good nutrients (and pods!) from the display as possible, and then let the skimmer pick up whats left over.
Some people even T off the overflow so that the water heading to the refugium doesn't go through the filter socks. This method is to save some of those pods that are coming from the display that would otherwise be caught in the filter socks and get thrown away. Check out some of the higher end manufactured sumps from Trigger and Eshopps to get ideas for layout.
For making baffles, I had good success just going to a local glass shop and having them cut me the glass to the correct size. Just make sure you get aquarium safe silicon and be generous - remember that bubble traps are your friend.
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