The answer in case anyone else is wondering.
To keep dolphin from auto-generating the controls for you map each time (for gamecube and wii respectively), put these lines into your system/recalbox.conf file:
##Keep dolphin emulator from overwriting custom config files
Now put the controller map you want to use into these files:
I use dolphin to create one profile and then duplicated it within these .ini files. That worked great for my purposes.
I found the answer here. Apologies for the double post, but I did not find it before in my search. https://forum.recalbox.com/topic/14345/dolphin-emulatet-wiimote-settings-are-reseted-every-startup