Random Forest Supervised classification using Graphy

yes, I recommend using a shapefile containing both classes as a text attribute (for example as described here)

Planning to automate is reasonable, but for the creating of a prototype you should first make sure that each of the steps takes the output of the previous step as a valid input. I recommend to test this first before creatign graphs. Once this works from start to the end, you can gradually build larger graphs until you have correctly connected the entire workflow.