Apps are kept on the internal drive, along with the operating system. Though as I said before, with the new high-speed interfaces it probably wouldn't make much difference.
You keep your entire "Home" folder on the internal drive so you're not messing with your Library folder being on an external drive (though theoretically that would be possible too). Just put your data stuff on the external drive. For some things you can use aliases to direct files there. I am not running a newer OS so I don't know if symbolic links work the same way anymore.
For me, photos and A/V media are the big space hogs. I keep those on other drives.
This is just the way things have to be done with new computers. Flash storage is fast but not particularly cheap, so most people have smaller internal drives. I guess in theory we would all subscribe to large amounts of iCloud storage and Apple Music, but I make do with the 5 GB free. In fact if you read the fine print even Apple says to make sure you back up your files on local storage.