Procedure to calibrate Z-home / limit. Repetier Host.

I've just built my first 3d printer, an prusa I3. And everything is working, I guess, but I have some problems with the procedure to find the zero position for the Z-axis.
I have a limit switch at the lowest position.

When I send the Home-command the nozzle crash into the heatbed before it finds the limit. Then you might ask, why set the z-limit switch below the heatbed?!
well, that because the Z-axis still gets a zero-position above the heatbed. Even though the nozzle is pushing the heatbed down, maybe half a mm, the distance between the nozzle and heatbed is still at least 0.5 - 1 mm ABOVE when done.

So, i guess there is some calibration/configuration that has to be done here. Can someone help me in the right direction?

move x axis home first or manually to the right the nozzle should be beside the bed now not directly above it do a z axis home it should come down beside the bed slide the extruder over if it hits the bed lift the z axis in manual mode raise the limit switch and repeat until homing the z is about 1 mm from bed then use the screw adjust on the z limit till you get 0.1 mm above the bed when you home the z. Now you have to level the bed all four corners to 0.1 mm (paper thickness). If you find one corner too low use that corner to fine tune Z axis home and re level bed. Before you start adjust bed screws till they just add tension to the springs and do the above without any auto level

I'd suggest you to move the z-limit switch to the top and change the firmware configuration accordingly. This way homing is done to Z_MAX and zero level is defined by Z_MAX_LENGTH in software which can easily be adjusted.
Having to align the physical position of a switch to the printbed is way more complicated, even when you have screws for more accurate adjustments (most cheap i3 don't even have screws for fine adjustments).

Btw. what you see when you're done is not Z=0 because usually the printer backs off few mm after homing.