it's up to you where you want to place the baffles.
i'm not sure that lowes has thick enough plexiglass though. i bought the thickest they had for my first attempt at a sump with refugium a while ago, and it bowed when i filled it. i would suggest glass. they'll cut it for you there as well, and it won't bow.
just remember, you'll need some space around the footprint of whatever skimmer you get, and then you'll want a decent sized refugium, so atleast 1 baffle in the beginning, then a series of baffles after the refugium to stop any bubbles from getting sucked back up the return.
also be aware that all evaporation will happen in the last compartment, where your return pump sits. unless you have an auto top-off, you'll need to have that big enough so it won't run dry if you can't get to it to refill it right away. depending on the climate where you are, your lighting, if your tank is topless or not, will all play a part in how fast that last chamber empties.
here is that first sump i attempted. the problem with it was, i had it opposite of what i am suggesting to you- the return was furthest from the tank. amazingly, i didn't get any bubbles in the tank unless i let the return area level go down alot, but it's better as i have illustrated in red.
the last baffle is raised up a bit so the water can run underneath it. the idea is the water will go to the bottom, but the bubbles will float up and never enter the return area.
you might even want to duplicate that last section, so that you have a series of raised and lowered baffles, if you have the room/patience/money for it.
if you click on my build thread below you'll see how i did the sump i use now. very simple, but then again, that return area is much larger, so i'm sure not to get bubbles.
hope that helps.