There are two direct ways to enter cheques in QBO. Well, actually three if you include creating a cheque in the Pay Bills process, but that aside, Entering a record of a cheque restricts you to using a bank type account, whereas entering an expense can be from any bank account as well as any current other asset type account, including credit card accounts.
You can enter cheques through the Expense screen and it will record the same as a cheque. Just remember to enter the cheque number in the reference field and the fact that if you need to print the cheques they do have to be creating in the cheque entry screen and not the expense screen (you cannot print a cheque created in Expense) Other than that, as long as you do not actually perform data entry twice, or add from a bank feed something that should be matched instead then you will not be duplicating anything.
Let me touch quickly on writing cheques for entered bills. If you manage suppliers and enter received invoices as Bills to pay later, DO ONLY use the Pay Bills option as writing a check through other means will not correctly "pay" the outstanding bill
