There are a few different ways you can work in QuickFile. Your method is absolutely fine, it will just mean that you need to complete any missing entries on your bank and manually tag them (there is a specific option for VAT payments). This process is known as bank reconciliation.
The other method is to setup a bank feed or import your bank statement from a spreadsheet file. Then your bank statement will be complete, but you will need to tag each item to explain whether it’s say a sales invoice payment, expense, tax payment, salary deduction etc. You can say for example raise your invoice as normal without marking as paid, then import your statement and link the money in on the bank as a payment to the invoice.
We work with a partner company called Yodlee for automatic bank feeds, you can find out more about this feature here:
We have a section in our Knowledge Base “Getting Started” that you may also want to refer to.