@Fin is correct....it's GE Slicone I that is the "safe" hardware store silicone.
DO NOT USE GE SILICONE II. What's also important is letting it cure for as long as you can.....I'd say a minimum of three days, but would prefer even a couple days more.
As far as the design of the sump (size of each compartment and location), that will be dependent on the drain configuration and the size of the equipment you wish to fit into the sump. First and foremost is your skimmer. You want to be able to fit your skimmer, and also have the room to take it out of the sump. I've seen folks who made their skimmer compartment to just fit their skimmer, and once installed in the stand, could not get their skimmer in or out of the compartment.
I too have a 90 gallon DT with a 40 Breeder sump. I have three compartments with no bubble traps. I found that I really didn't need them. I only get bubbles from the water cascading over the baffles...nothing from my skimmer. I also have two drains....one is each back corner of the sump, with the return section in the center of the sump. Here's a picture of my 40 Breeder:
One more calculation you'll need to do is to determine the amount of water flowing back into the sump once your pump is turned off. I always get people commenting that my baffles are too high and my sump will overflow. Well I calculated the amount of water and it comes right to the top of the baffles....fits just fine.
Planning is critical to a great sump! Know what you want to do.