The production of top quark pairs in association with heavy Standard Model bosons or with heavy flavour quark pairs is important both as a signal and a background in several ATLAS analyses. At present, strong constraints on such processes cannot be obtained from data. Therefore, their modelling using Monte Carlo simulations as well as the associated uncertainties are of critical importance. This work documents the Monte Carlo samples currently being used in ATLAS for $t\bar{t}H$, $t\bar{t}V$ ($V~=W,Z$ vector bosons) and $t\bar{t}$+bottom quark pair processes for $\sqrt{s}$=13~TeV proton-proton collisions.