Thank you for reaching out to the Community. Undeposited funds can show a negative value on the balance sheet if payment is deposited, with a date that pre-dates the payment. If a balance sheet run between those two dates, It will show a negative. Let's review the payment and deposit to make sure they have the correct dates.
It could be since QuickBooks Desktop automatically holds the funds in the Undeposited Funds account when receiving payments from customers. To clear the amount in this account, you’ll need to make deposits.
Let's create a journal entry and deposit the payment to zero out the balance. Here's how:
Go to the Company menu and select Make General Journal Entries.
Fill out the fields to create your journal entry. Make sure your debits equal your credits when you’re done.
Select Save or Save & Close.
Now let’s deposit the payments. Here’s how:
Go to the Banking menu.
Select Make Deposits.
Select the payment in the Payments to Deposit window.
Choose the bank where you want to deposit the funds.