
You should really engage your site administrator(s) of your tool. They should be aware of the integrations being performed. More than likely, they have a service account available for your use already.
If the admins don't know you're doing what you are doing, when they go through upgrades, conversions, etc they won't engage you or your processes.
What is your particular administrators preference on how to accomplish your integrations?
With regards to integrating with ANT, when you're using the command lines it doesn't really matter if you are using ANT, shell, etc; the command line utilities still have requirements of their own.