Which are the initial values of Q1 and Q2 values of the KiBam model in the beginning of the simulation period? May the selection of those values affect the result somehow?

HOMER assumes that the battery starts at 100% state of charge, so the initial value of Q is Qmax, and the initial value of Q1 is c * Qmax.  The equation Q = Q1 + Q2 always works.

The assumption that the battery starts full could have a measureable impact on the results in a system where the battery is very large, but in most cases the battery autonomy is a matter of a few hours, it will not significantly affect the results over the 8,760 hours of the simulation.