"So as first step I need to import 2 gerber files to the tool. I think I run into issue where we have the same layer name and the layer imported before is over-written. Is there a way to bypass this limitation besides manually change the layer name? I tried creating new job, but it doesn’t seem to help. I’m pretty fresh on this tool so would like guidance here."
Since the gerber files have the same name, there are several options:
Use Compare Jobs.
Use Compare Layers.