You will not lose your spot on the Section 8 waiting list due to a debt, unless that debt is to a housing authority. Housing authorities don't usually require a credit check (though they do require a criminal background check) for the Housing Choice Voucher program.
However, you should make sure that your payment agreement with the landlord is well documented on paper. Make sure to save all of your payment receipts. If there is a public record of that debt to a landlord, you should ask them to remove the record when you pay it in full.