Before 3.15 I *think* I had a panel going across the bottom. I think with an upgrade all that stuff goes away. Or maybe it doesnt, havent touched my PB G4 in quite some time. In my previous version where do I copy those prefs from?

Updating MOS does'nt touch any of your private settings (located in SYS:PREFS/....)
MOS only replaces folder SYS:MorphOS (and propper boot.img, of course!)

Yeah these should be preserved in system update, but if you want to make a backup, Ambient related prefs files can be found in SYS:Prefs/Ambient/