I have a Century III autopilot, already have a G5 ADI and GTN 650, and am planning the HSI in a couple of months, so this probably holds true for both of us:
In the setup you describe, assuming a GAD29B is in play, the GTN650 can send GPSS directly to your AP if you leave the AP's mode select in "HDG" mode. If you switch it to NAV/etc., it'll work as usual, just using the steering guidance from the HSI instead of the KI-209 or 206 (I'm assuming you have one of those for your King CDI paired with the KX-155, which I also have.)
I do not plan to let the autopilot "see" nav #2 (which is the KX-155 I mentioned), instead leaving that connected directly to my existing KX-155. I imagine one could install a switch to let the AP be driven by radio #2, but to me that seems unnecessarily complicated, and something I'd rarely use. If I lost the G5 or the GTN650, it's true I'd lose AP nav and approach capability, but it would still work in heading mode, which is plenty good enough for my purposes.
At least that is my current thinking.