We investigate the mechanisms of CoSi2 and CoGe2 growth by carefully controlled e-beam evaporation of Co onto Si(001) and Ge/Si(001) substrates from the very initial submonolayer stage,. monitored in situ by scanning tunneling microscopy, aided by reflection high-energy electron diffraction. In order to grow different epilayer morphologies, we use flat and vicinal surfaces and two different methods of synthesis: reactive deposition (where Co is deposited onto a hot substrate), and solid-phase reaction (where Co is deposited at lower, or room, temperature). We attempt to account for the observed morphological differences in the epilayers by correlating them with parametric differences in the deposition and growth processes.