Here's the briefest summary of how non affiliated scanning works. This presumes you have solved all problems relating to access to system keys of any required type.
Here's the operational summary:
Create a zone that contains 16 conventional channels in slots 1 thru 16. And trunked systems in slots 17 thru whatever.
Trunked systems are NEVER NEVER NEVER placed in slots 1 thru 16 on ANY zone. They stay above 16, where they can NOT be accessed via the rotary knob.
The beauty, the glory of it, the thing that makes it all possible, is that a conventional channel can have a scan list attached to it that contains only trunked talkgroups. We're going to abuse the heck out of this feature!!!
Channel 1 is conventional and slaved to trunked scan list 1.
Channel 2 is conventional and slaved to trunked scan list 2.
Channel 3 is conventional and slaved to trunked scan list 3.
----and so forth----
Channel 16 is conventional and slaved to trunked scan list 16.
Channel 17 (and higher channels) are trunked personality entries, the ones referenced by the trunked scan lists.
Repeat on each zone as needed.
To be clear about this, for safety's sake, there is no CHAN or SUB menu entry in the radio which would ever allow you to directly access above channel 16 in any group. This makes it impossible for the radio to affiliate on any trunked system programmed in the radio.
You do need to keep very careful track of how the slaved scan lists are configured and assigned.
Scan characteristics need to be paid attention to as well. (Priority settings, etc.)