I discovered a little trick for changing the menus before activating with JonRadio Multiple Themes.
I was originally UNsuccessful doing this with the Theme Test Drive trick described in the FAQ. I tried multiple times.
But using WP's built in Theme preview functions, I was able to change the menu item successfully. I had to briefly "activate" the theme in WP, then deactivate, but it worked. Hopefully this will help others:
Click on: Appearance --> Themes --> Live Preview the theme (in my case "Skeleton Child Theme.")
Under Navigation, I selected my Primary Navigation to the the same as my active theme. Then I clicked "Save & Activate."
I then reactivated my primary theme, and went into JonRadio MT to activate Skeleton Child Theme for one particular section. It worked!