My Z axis homes at the bottom and I focus on a platen that the laser frame sits on. I guess it's about 70mm. With it focused there, I simply jog up the Z by the thickness of the workpiece. No need to mess with the lens focus. If the material is more than 40mm (max travel on Z) then at the moment I put the whole frame up on spacers and adjust the Z height accordingly.
double print issues are called backlash. You can fix it by making adjustments to your x axis. Adjust belt tension and wheel tension. The belts may need to be tighter or looser. The wheels should roll smoothly. If you raise one end of the machine with it off it should slide to the other side. If it doesnt the wheels are too close to the rail and binding.
I have so much trouble with my A3 pro until I got in touch with Zax and between us we solved the problems, I'm not sure there's a great deal of difference in these programs, but what I am sure of the backup and support you get using T2Laser cannot be bettered, it's a small amount for the program but if you get into trouble Zax the man to solve it.