Hi Brian,
you can ignore (if you want) warnings, but not errors in red. As long as there are errors, code is not generated/updated, so you have to resolve the errors.

You indicate that you are changing the muxing during runtime
For switching muxing at runtime you can create functions. For this you add a 'tab' in the routed pins view (you can give each tab its own name):


That way you can have both sub channels be configured, as they won't be active at the same time:

And you have two functions (named after the tabs) you can call for the muxing from your application:

I hope this helps,
Erich