A helpful way to think about it is to consider the “Prepare” tab more like an overall project, that can include multiple plates and multiple color combinations. When thinking about the slicer in the traditional way, it can feel weird, but when you think about how you can organize a larger/more complex project within there, it makes more sense. Since changing my way to this thinking, I haven’t synced the AMS at all. (where it syncs what’s loaded into the slots in the prepare page) Although I do select filaments from the dropdown, from ones currently loaded. That’s just convenient though.
I have a few projects I have split up between multiple printers. Each one has their own filament loadout. Those loudouts don’t necessarily confirm to what I have setup in the slicer. I set the slicer up so each plate is setup with the settings I need, and the color palette I want for the parts on that given plate.
When I go to print, I usually just load up (if they aren’t already) the colors I want into the AMS, and the slicer slots everything in where it needs to go.