Dear @asantra
I am not entirely sure we are on the same page, so let me try to shed some light on the details here. You are using the DepositionReader module which allows you to read in energy depositions in your sensor material, simulated already in a different software tool. This means, what has been done already is the simulation of
- the initial primary particle creation
- the tracking of this particle through your entire setup
- ionization processes
- the possible creation of secondary particles
- multiple Coulomb scattering processes
and the output of this has been written to a file which we now process with the DepositionReader. Allpix Squared does not take any assumption an where charge carriers are created, but it simply reads in energy deposits from another simulation and transforms them to electron-hole pairs. If this is not the case for you (as you might have indicated in your previous post) then this module is not the one you should be using, but probably rather DepositionGeant4 or the like.
This module is not meant for reading the total charge of a particle passing through the detector, but the result of a more fine-grained simulation also telling us where in the detector the energy was deposited.
Since this is all happening in the upstream simulation tool, your question 2 has to be answered there. 
Now, what we read in with this module could look like this (CSV file version):
# pid, time(ns), Edep(keV), Px(mm), Py(mm), Pz(mm), volume, trackid, parentid
Event: 1
211, 3.528537e+01, 4.412099e+02, 1.171342e+01, 6.526809e+00, -2.497500e-01, detector2, 0, 0
211, 3.528575e+01, 5.422071e+02, 1.171451e+01, 6.527448e+00, -2.487423e-01, detector2, 0,0
Event: 2
211, 3.234674e+01, 1.091620e-02, -2.515335e+00, 4.427924e+00, -2.497500e-01, detector1, 0, 0
11, 3.234697e+01, 1.797317e+01, -2.530000e+00, 4.453741e+00, -1.914370e-01, detector1, 1, 0
11, 3.234698e+01, 2.138917e-01, -2.530711e+00, 4.455000e+00, -1.885962e-01, detector1, 2, 0
11, 3.234747e+01, 3.317139e+01, -2.561796e+00, 4.510000e+00, -6.449268e-02, detector1, 2, 0
In both events with energy deposits, we have initial pions (PDG 211) and in Event 2, there are more energy deposits by particles with PDG 11 (electrons) which link to the primary particle.
Now what I mean with “first” and “last” appearance is that the first energy deposit entry where a new track ID appears marks the start point of the respective particle, and the last one in the event in which it appears is taken as the end point. Please mind that this doesn’t have to be entry and exit points sicne the particles might well have been generated inside the detector (as happened in the case above, sicne they all link to the primary pion with their “parent ID”.
Does this clarify things for you?
Best,
Simon