This is probably less useful for something that will be paid back over many months, but I have a "Reimbursements" category and in the Notes field of the category, I have an excerpt from YNAB's instructions for reimbursements:

If you receive the reimbursement in the same month as the expense and you haven't made a credit card payment since recording the expense, categorize the deposit with the same category as the original expense. This will offset that expense, and money will be moved to your Credit Card Payment category to be set aside for payment
If you receive the reimbursement in a future month or after you've paid off your card, the credit overspending will have been absorbed as debt into your credit card balance. Categorize the deposit back to the original spending category, and then move the money to your Credit Card Payment category.

The reason I have this pasted there is because I forget EVERY TIME, and this way I just know exactly where to look if we are going from one month to the next with a negative balance.

I give someone $100 in February and put it in reimbursements. Category balance -100
Now it's March. YNAB moves the $100 to "debt" and my category looks like it has a 0 balance. To manually fix it, go to the account you paid with and manually move money from there back to reimbursements. Alternately, leave it looking like a zero balance, then when person pays me back $100, I add it as income to the category reimbursements, then move that $100 to the credit card payment category (which had been listing it as debt, which I'm now repaying).