Export you gerber mirrored. Export your drill file mirrored. Load Gerber into Flatcam Load drill file into Flatcam. I like to adjust the offset at this point. Click on the gerber object that was loaded. Set tool width and number of passes Press generate geometry (this creates a iso objest). Note you may want to first check combine passes. Click on you Excellon object and set you various parameters. Click on Generate. This creates a CNC object for the drills. Click on your iso object for the traces. Set your various parameters and press Generate. This creates a CNC object for the traces. Click on the cnc object for the traces. Press Export gcode Click on the cnc object for the drills. Press Export gcode. Flatcam is very non intuitive imho. But far, far easier than trying to load your drawing into Eagle to use pcbcode, if you don't use Eagle. And Flatcam is eaier to user than Coppercam imho.
And once you get used to all of the steps, FlatCam is actually very easy to use.