I'm trying to setup my own custom race, but I'm a little confused on how languages work. If I add a Trait/Modifier to give a Language to a race, it just gives it to them as far as I can tell. This means they automatically speak it by default. But what about the bonus language pool? Is there a way to specify certain bonus languages that are applicable to this race to learn? I think some classes operate this way. I saw a "Choose Language" option as a Modifier, but I assume that just gives the player an auto choice of any language available, not alter what their options are.
Yes, the choose language option allows a choice of any available including any custom languages. If you wanted you could just simply add the language you have created to choices that allow extra languages