Assuming you want to record the payments on QB and if the version is 2008 or 2010 Pro, then the best way is to file the VAT returns in QB quarter by quarter. When you do this QB creates an invoice to the HMRC supplier account which you then pay as a normal invoice.
If you are not recording the payments on QB then you'll have to do it another way, which I'll have to think about... :-)
Pauline
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