Hi Debbie - you probably have this sorted by now but just in case......
Yes you are right; the balance of the VAT control a/c at the end of the VAT period you are dealing with should be the same as on the VAT return.
You probably kmnow this, but in QB when you submit the VAT return this balance is automatically cleared by a journal to/from VAT suspense a/c which in turn is cleared after the VAT is paid (or received in the event of a refund).
This journal is dated the same day as you submit the return so what I do is go into the VAT control account, find the jourenal and redate it the last day of the VAT period you have just dealt with. As at that date the balance of VAT control should now be nil.
When you start the next VAT return
1) check the balance at that date is still nil
2) if not a transaction reported on a previous VAT return has been changed
3) check that change is reported and explained in the VAT 'exception' report and that you are happy with it.
I hope this helps.