So with the awesome help from bot libre, i've got my bot almost to the point where I'm ready to deploy. I figured out how to get the bubble to go away using some CSS (the checkbox doesn't seem to work on embed.)
I have a couple of remaining issues.
1) In live chat, my bot won't auto-repsond unless the visitor types accept first. I want the bot to respond as long as it has a high confidence response.
2) The tool icon next to the chat get's squished, and sometimes disappears. This is probably something I can fix with CSS but wondered if anyone else had experience as my CSS and HTML are intermediate at best.
Once I get these last two issues resolved, I'll be read to deploy and start training my bot and serving guests.