I did this by renaming the "bones" folder in /opt/zimbra/jetty/webapps/zimbra/skins/ and creating a new "bones" symlink pointing to my favourite theme - in my case, fields.
This is my one-stop script for downloading and installing Fields, and replacing Bones with it. I run it after every upgrade:
No responsibility accepted for anything this might break. Seems fine on my servers though.
mv 114 fields.zip
zmprov mcf +zimbraInstalledSkin fields
mv bones bones.orig
ln -s fields bones
note: run script as zimbra, not root.