So... here is my advice. First back up everything when you get it, using FractalBot.
You will always have access to Fractal Factory presets from their website, as well as the original download files from the Naked Amps.
Next, there is a blank bank in the 1400+ Naked Amps TonePack. Load that into Bank A. It will overwrite everything, that's okay. You are going to be using Bank A as your own FAVORITES bank, using Axe-Edit.
Next, load the Factory Bank 1 or A into Bank B on your Axe-Fx III. Spend some time checking out the Factory takes on many popular amp models. Factory Banks B and C are very cool but are heavy on effects and showing what the Fractal can do. They aren't real basic live/club presets.
Then load each Naked Amps bank 1 and 2 into your Axe-III's Bank C and D slots, using FractalBot (one bank at a time). You now have three banks of great amp sounds!
Start checking out amps using Axe-Edit. When you find an amp you love, simply copy and save it into your own Axe-III's Bank A - start filling that up with your chosen "Keepers'.
When you've gone through all the Factory Bank A presets (residing now on your Axe-III's bank B), and have saved the ones you like into your personal "keepers" Bank A, then you can overwrite the Factory Bank A (in your Axe-III Bank bb) with Factory Bank B - -then check that out....then later do for Factory Bank C.
My other advice is, when you hear great EFFECT in the Factory presets - a great delay, reverb, rotary, etc. -- save the BLOCK for it (start creating your own effects block library), so you can access it and put it into your own presets.
Etc. This is just one methodology...