Los Lobos Marinos' suggestion is exactly what I would have recommended. You essentially "created" money in your budget by going into debt, and budgeting the negative amount to the debt category neatly captures this while giving you a place to budget for the repayment. You would then budget this money to the categories in which you overspent (spent more than you had in the category balance) to eliminate the overspending. I would add that if you already have a Pre-YNAB Debt category for this card, you can use that instead of creating a new category.
Your payments to the credit card are a transfer with no budget category. The spending has already been categorized by either the debt category or your other budget categories, so categorizing the transfer would count this against your budget twice.
Hope this helps!!
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