Hi Sam,
The Double-sided PCB tool in FlatCAM has two functions. One is to mirror a layer and the other is to create alignment drill holes. It is key to have the same mirror axis for both the mirroring and the alignment holes. If your bottom layer Gerber is not flipped, then FlatCAM will flip it for you. If it's already flipped, you don't need to do anything further (Assuming that your CAD program did things right). If you want the alignment drills though, you must figure out exactly how your CAD program flipped your board around and your can enter this data into FlatCAM.
You may also want to "un-flip" (or flip again) your bottom layer in FlatCAM, just to see that it aligns correctly with your top layer.
I will try to clarify the manual, perhaps with some diagrams.
Thanks,
JP