Marlin bed autoleveling confusion I've just added a Z-Probe sensor to my custom printer (Arduino - RAMPS 1.4 - Marlin 2 default disabled EEPROM) but now I'm confused. Printer seems to work but I cannot configure the right nozzle height.

I use Pronterface and before start printing I send G29 code. Printer succesfully ends bed calibration. At this point I start printing but the printer seems to ignore the calibration (no bed compensation). 

Do I need to run other commands to tell printer to use the previous calibration?
When the printer ignores the scanned topology (grid) of the bed this means that the levelling is not active. G29 activates the M420 to enable the grid. A G28 after scanning the bed will reset this.

You need to make sure that the start G-code (this is an optional script that is pasted before the sliced object) contains both the G28 and the G29, where the G28 is placed above the G29 on separate lines.

For each slicer this is defined in different places, bit if you use Pronterface for slicing, a good chance is that it uses the Slic3r engine. If I open an STL for slicing in Pronterface, it starts loading Slic3r.exe; this brings up the GUI for Slic3r which has options to define/modify the start G-code.