When I click in the Appearance menu to color a stroke or a fill, it pops up a library of swatches. I can't figure out how to get that to show a different swatch library. I have a saved library, I can even made it pop up in a different window, but I don't know how to make it show up in that specific window when I want to change/set the stroke/fill color.
The Appearance Panel color popup is only designed to show the default Swatch Panel, or the Color Panel with a shift-click. You can not change it to show a custom swatch library. It will only show items in the Swatch Panel.