So, as you've figured out, the surface object is pretty useless unless you're modeling shear walls.
A better option for you is the "create parametric model" option under geometry. It works pretty well for creating meshes. You can assign nodes or beams within an area as density points. I haven't had any luck at inserting holes in parametric models, it normally crashes, but you can insert beams around your hole and then delete the resulting plates created inside the hole area pretty easily.
After making a parametric model you can merge it into your model and the result is a bunch of standard plates upon which you can assign a thickness.