That would work if you don't plan on putting any sand in the refugium area at all...
If you want to put sand in there for a specific species of macroalgae that requires a sandy/rocky substrate, you may want to put your first baffle 1" up and your second baffle all the way down. But, if you are growing chaetomorpha algae, then you will want to go with your original design so that it has some ability to "turn" as is grows....
BEFORE you begin,... take some sandpaper and lightly sand the edges of the glass. It will keep you from cutting yourself while you are working with it ... and working in your sump later. Trust me, after getting sliced open a few times and getting saltwater in the cuts while doing maintenance, you will curse yourself for not using sandpaper. lol The Dollar Tree usually has sandpaper in the hardware section... and it will work for your purposes,... unless you already have some laying around.