well, for me i use the global axis offsets to set my z height in simplify3d. for example, and i've only been using it for 3 days now, i set the global z to be -0.05mm and save this with my profile. it's easy for me to adjust there. i've stayed away from setting things via marlin or the printer's control box. although on my printer and marlin, i can baby-step z while it's printing the skirt/brim. but mostly i'll just print a whole first layer see how it looks and then adjust in the software.