Append the end of your Pro/E startup command with -g:no_graphics.
Pro/E can do anything in no-graphics mode that doesn't require user interaction. J-Link, Web.Link, trail files, Pro/TOOLKIT, Automation Gateway, all these methods work in no-graphics mode. I'm not sure, but would imagine Pro/BATCH can run this way too. Test your applications in graphical mode to make sure they run smoothly before going to no_graphics. Its hard to debug something you can't see.
The benefits of no-graphics mode is it doesn't take up as much memory. It doesn't take as long to load, and it runs much faster than a normal session.
The drawbacks are: It still draws a license of Pro/ENGINEER. You can't interact with the session. When your task completes/fails, you have to close Pro/ENGINEER. You can code your app to close Pro/E or you can close Pro/Evia the task manager.
If you don't have any Pro/ENGINEER licenses to spare, PTC used to and may still sell an E-ENGINEER license. It is Pro/ENGINEER without the UI. It's cheaper than a regular Pro/ENGINEER foundation seat.