You can silicone strips of glass to the sides and baffle to create a ledge for your acrylic filter sock holder.
Bubbles don't stick around in freshwater as easily as saltwater, the idea with bubble traps is to keep bubbles out of the pump, but that's just not needed for freshwater.
Typically the idea with filter socks is that they are setup to be easy to remove and wash, so you use them to catch the gunk to keep the rest of your sump cleaner. The way you are planning will work, just not typical.
Make sure you have enough surface area to flow through your first set of filter foam - water needs to build up to a certain pressure to get through filter media at a given velocity - your design will have very low pressure at your course foam pre-filter, and making the area larger will reduce the flow velocity through the foam. If it can't get through, the water will overflow into the biomedia chamber and bypass the prefilter altogether. I attached a drawing of the media in my sump (it is split down the middle, so after going through this, the water flows up and over the center baffle into the pump chamber that takes the other half of the tank.
If your sump and main tank are both covered, evaporation loss shouldn't be too bad - my main tank is rimless and topless, so I had to consider it. The consideration is that the water height loss due to evaporation is all in the pump chamber, so if you think you would loose say 1/2" to evaporation in your main tank, and surface area in the main tank is 5x the surface area in the pump chamber, you will loose 2 1/2" in your pump chamber and the main tank will remain stable.
-Justin
-Justin