This example demonstrates how the chemnum package can be used to automatically number compounds in reaction schemes created with ChemDraw (saved as .eps files). While the chemstyle/chemscheme package can also be used, its author recommends the use of chemnum as it's deemed to be clearer.
Ideally, the ChemDraw-generated .eps files should contain "TMP1", "TMP2" etc as temporary markers, which will then be replaced with automatically incrementing compound counters using the \replacecmpd command. Switch the LaTeX engine to LaTeX+dvipdf from the project's Settings icon (the gear icon) so that the replacement actually takes place.
This example shows how a striking chemistry presentation can be created with a few simple LaTeX commands.
I've used two great chemistry packages that are freely available for LaTeX: mhchem and Chemfig
to create the diagrams.