I have a MacBook with Japanese keyboard (physical), I use Google Japanese Input as my main input system. It lists three keyboard layouts Alphanumeric, Hiragana, Katakana in the settings ¥¥Keyboard -> Input Sources.
I also created a custom layout using Ukelele Mac OS X Keyboard Layout Editor. This layout works perfectly and I never had to intentionally switch to another Input Source.
It seems though, that for Japanese characters to be entered (in my layout), the Google input sources must remain present. In some rare cases my input automatically gets switched to one of the Google layouts, requiring me to switch manually back to my custom layout.
The question: can I somehow leave Google IME "operationally" active, but prevent it from being selectable as an input source?