To activate the Auto-Tune with a PC5, you just check one box. You never really see the AutoTune as a device. It is an extension of the PC5.
Hook up your PC and start the bike. After about a minute of warm up, you should start seeing AFR readings on the right, one per cylinder. If they do not show up, the AutoTune is not connected properly.
When you read the map from the PC5, you should now have Trim Tables visible, one per cylinder. This shows the variance from the map that the AutoTune is reading. Positive numbers means add more fuel, negative numbers mean add less fuel. This is actually done by changing the injector cycle time.
You can update the operating map by applying the trims. This changes the default map to incorporate the trim changes. At some point, the trims will become small numbers (less than +/- 5). At that point, the AutoTune has pretty much dialed it in. Just remember, when you ride, there are some cells in the map table you will never hit, some you will hit only under certain riding conditions (hills, straightaways, curves) so make sure you do a lot of different riding before you think it is dialed in.
Once dialed in, you can shut off the AutoTune if you like. This avoids any glitches, the map is set. I added a switch under the seat to turn mine on/off. It has been off for over a year now. If you make a change (pipes, intake, cams, whatever) turn it back on and let it retune.