So nobody has ever explained what to do regarding VAT payments on sage to me.
I am guessing that for the Quarter i would journal what I have in Purchase Tax and Sales Tax and post that to VAT liability and then post the cheque payment to HMRC to VAT liability also?
Yes you can do this via manual journals as you have descibed but the easier method is to use the VAT wizard.
This is found in Modules -> Wizards -> VAT Transfer Wizard.
YOu need to check that the amounts being posted to the Sales tax, Purchase tax and VAT Liability are the same as the amounts shown on the VAT Return used, but if these are ok, it works fine.