You can use acrylic for the baffles. Our local Lowes cuts it to size for free. Placement depends a lot on what you want in your sump. For the bubble trap I used 2 standard sized CD casesfor separation and 3 cases for the height from the bottom of the center baffle. You also need to know what equipment you want in the sump such as the heater(s), grounding probe, temperature probe, dosing pumps, etc. Here is an idea I had for when I re-do mine. One thing you MUST keep in mind: Use GE Type 1 100% silicone or equivalent when you seal in the panels. Do not use anything with mildew inhibitors, colors, or any other additive. they are usually poisonous to your fish.
Why do I love fish? Because every time I stare into the little world I have created for them, every problem I have just floats away....