We present an upgraded version (denoted as version 2.0) of the program HELAC-Onia for the automated computation of heavy-quarkonium helicity amplitudes within non-relativistic QCD framework. The new code has been designed to include many new and useful features for practical phenomenological simulations. It is designed for job submissions under cluster enviroment for parallel computations via Python scripts. We have interfaced HELACOnia to the parton shower Monte Carlo programs Pythia 8 and QEDPS to take into account the parton-shower effects. Moreover, the decay module guarantees that the program can perform the spin-entangled (cascade)decay of heavy quarkonium after its generation. We have also implemented a reweighting method to automatically estimate the uncertainties from renormalization and/or factorization scales as well as parton-distribution functions to weighted or unweighted events. A futher update is the possiblity to generate one-dimensional or two-dimensional plots enco...