The design of plasma acceleration facilities requires considerable simulation effort for each part of the machine, from the plasma injector and/or accelerator stage(s), to the beam transport stage, from which the accelerated beams will be brought to the users or possibly to another plasma stage. The urgent issues and challenges in simulation of multi-stage acceleration with the Apollon laser of CILEX facility will be addressed. To simulate the beam injection in the second plasma stage, additional physical models have been introduced and tested in the open source Particle in Cell collaborative code Smilei. The efficient initialisation of arbitrary relativistic particle beam distributions through a Python interface allowing code coupling and the self consistent initialisation of their electromagnetic fields will be presented. The comparison between a full PIC simulation and a simulation with a recently developed envelope model, which allows to drastically reduce the computational time, will be also shown for a test case of laser wakefield acceleration of an externally injected electron beam.