Enter budgets according to the normal balance of the account. If the account code is for a Contra account, the normal balance will be opposite the balance for regular accounts in that category.

For example: A contra-revenue would have a debit balance.

Enter budgets as positive if they will be the normal balance for the account. (In the example above, if a debit balance is expected, enter a positive number for the budget).
Enter budgets as negative if opposite the normal balance is expected.