If you want to override any of the default behavior, just add a new file (ending in @.fish@) into the @custom/@ directory.
If you want to override any of the default behavior, just add a new file (ending in @.load@) into the @custom/@ directory.
If you have many functions which go well together you can put them as a *.fish file in the @custom/plugins/@ directory and then enable this plugin.
If you would like to override the functionality of a plugin distributed with oh-my-fish, create a plugin of the same name in the @custom/plugins/@ directory and it will be loaded instead of the one in @plugins/@.