Dear Moritz,
for implementing a source routine, you can take a look at the new version called source_newgen.f, available in the latest release FLUKA 4.1-0.
It features a simplified way for assigning the beam parameters, and an extensive documentation is available directly in the source file, or in the FLUKA manual under section 13.2.20.bis}.
The Non-Zero Cells printing option means that the printing of the result is skipped, but the header for that event is still printed.
The solution could be the DETECT scoring, which results the energy spectrum in a region directly. The number of event can be calculated, if the energy range is selected correctly, by summing up the values of each bin. See: Question regarding DETECT scoring
Cheers,
David