Well, you would have to start by getting familiar with PrePoMax - doing some simple analyses following tutorials. Then check the Keyword Editor (also covered in some tutorials). For it, you need to follow the CalculiX syntax described here (each keyword is explained there and example .inp files are referenced - they can be found here).
You can also find some examples specifically for orthotropic materials in this forum thread:
Automation with other software would be the last step as it’s the trickiest part and you need to know how to define a model manually first. But geometry needs to be provided for PrePoMax, usually as a STEP file (recommended format) unless you import a mesh prepared in other software. I use FreeCAD to prepare the geometries but any CAD software will work.