Hi Laura,
I know exactly how you feel. I've recently become the point of contact for our Automic instances, but have a long way to go to reach the same level of comprehension as the previous individual.
To your question, I will second what Matthew stated. We have several teams that leverage a Windows agent to execute SSIS packages from the command line, using dtexec. My understanding is that these packages can be created/exported from MS SQL Server. So far I've not heard/seen anyone directly executing ssis packages from Automic (without dtexec in the middle) with SQL agent. Hope this helps!