I believe your questions are related to the FHI-aims calculator.
We should take great care not to confuse ATK with FHI-aims. ATK is a platform that includes several different computational engines, including ATK-DFT, ATK-semiempirical, and ATK-classical. FHI-aims is another engine for first principles calculations, developed at the Fritz-Haber Institute in Berlin. You can set up, run, and analyze FHI-aims calculations using the VNL interface, but your ATK licence must include access to FHI-aims for this to work.
1) FHI-aims accuracy is tuned mainly by increasing the basis set size and by using increasingly dense integration grids.
2) What matters is the expected electron distribution around the Fermi level of the full system, not the individual parts of it. Is the full system an insulator or conductor? In any case, both options may often work rather well.
3) ATK offers the Grimme DFT-D method, while FHI-aims also implements the TS and vdW-DF methods for van der Walls interactions.