How to remove credit card and it's debt
I no longer want to have the credit card as an account. It's a closed card and I simply want it to be in the debt category and submit payments. I was able to put it in the debt category just fine, but I can't get rid of the negative balance. YNAB tried to deduct the debt from my money and I don't want that. I had to delete the transaction. So now the card is closed but it shows up in my NET worth. And I don't want that either.
You're on the right track! To get rid of the negative balance, reconcile the card (on the web app), enter a balance of 0, and click Create Adjustment & Finish. This will zero out the card without changing anything else in your budget.
Then, hide the Credit Card Payment category for this card and create a new category for budgeting for the payments, if you haven't already. That should do it!