I just figured this out.
Press start on a second controller and the bee team should appear. Sometimes you have to press start again to reactivate them if they haven't moved in a while.
Use the control stick to move them. The bee team moves like a cursor on the screen.
When over a quill or butterfly, press A to grab it. You'll see a yellow swirl on the bee team if you collected it.
If you've grabbed a butterfly, press B to drop it. It'll reappear near yooka and Laylee so they can grab it!
There's no in-game instructions and there's zero audio feedback. I'm not sure if I'm missing something, but those are the basics of using the bee team.