The simplest way to record bank transactions that do not have an actual check written, like an automatic withdraw, is to do the following in "Payments and Purchases":
1) After select the items being paid for select "Expense and Other Payments" 2) Select the bank account and enter the amount being withdrawn as a negative amount. 3) Press "OK" and now the total purchase should be $0.00 4) Record the payment.
This will cause the correct amount to be taken from the bank account without requiring a check number. This transaction will not show up in check reconciliation to be cleared because it is automatically cleared when you record the payment.
If you want a reference number in the check register, you will need to record the payment using the "Check" button and use a fictitious check number ( #1 ). When you get your statement you change the check number to the correct reference number using "Check Maintenance" under "Cash Account Maintenance" on the "Accounting" menu.