You're using the Genre Category feature backwards - you should be mapping multiple Genres to a single Genre Category, not the other way around. More specifically, for your example you should have a Genre Category called "Ambient" which includes the genres "Electronic Music" and "Chillout".
Having said that, you could set up the tags you want quickly in Mp3Tag.
For your example you'd set the field custom_genrecategory
with the format string:
This says if the track genre is "Ambient", set your custom genre tags to "Electronic Music" and "Chillout", otherwise leave it as is.
Set up an action group with a "Format Value" action for each category you want to map.
(no warranty implied if you destroy all of your music)
Bee excellent to each other...