How do I make it so that input method is always set to one I actually choose?
I don't use Squirrel, so this answer may not necessarily apply.

Once you've added Squirrel as an Input Source in your Keyboard System Preferences (as you've already done), you should be able to make this the default in your Language and Region System Preferences.

More specifically:


Go to Apple > System Preferences
Select Language &amp; Region
Click + button at bottom left
Choose the appropriate language
When prompted set this to be your primary language
You may still be prompted to add an input source in your Keyboard preferences, if so just redo that as well (i.e. add Squirrel)
You may also need to restart your Mac