The Profit and Loss account on Sage will be excluding VAT. One reason for this is because when the accounts figures are submitted to HMRC they are normally reported excluding VAT.
VAT is collected by a VAT registered business, any VAT suffered by the business is deducted and the balance paid over to HMRC. Therefore the VAT payment each quarter is not actually an expense of the business.
Also the tax payment to HMRC for Income Tax is NOT a business expense and is also excluded from the Profit and Loss account. For a Limited Company the Corporation Tax charge will be shown as a business expense, and therefore you may wish to include this on the Profit and Loss account.
Payments to HMRC for PAYE will be shown on the Profit and Loss account either in with Wages costs, or in a separate heading.
Remember also that any payments to HMRC that are for VAT or Tax should be given the ‘T9′ VAT code, this will then ensure that they are NOT included on the VAT return.