Assuming you will be performing chemotactic invasions assays, you will want to use growth factor reduced (GFR) Matrigel to ensure that your cells invade towards the growth factor/chemokine conditioned media in the bottom wells and not respond to any growth factors within the Matrigel. Good luck!
It will be better to use GFR Matrigel, since you can be sure that the invasion is entirely due to the compounds rather than the growth factors (of which there are plenty) in Matrigel. Hope this helps !