Fractool will port the AFX II presets to your new AFX III, but plan to spend time going through each preset to check everything and tweak as necessary. Things WILL be different. In some cases not by much, but in other cases it can be pretty significant.
I ported my II presets to my III with Fractool to have a starting point, but as time has gone on, I've re-done pretty much all of them from scratch now. With things like channels and other new features in the III, it was good for me to re-think how my presets were set up and streamline things. (While making them sound better, too.)
As far as overwriting the factory presets, Just don't store your ported presets where the factory presets are stored. There are blank preset spaces in the upper numbers of the banks. Store your ported presets there. Or move the factory presets to the higher-numbered slots, and port your old presets to the low numbers.