AutoEntry gives you the ability to mark invoices as paid - please see here for the general guide on doing so.
For Sage 50 UK&I specifically, it is only possible to mark invoices as fully-paid (not part-paid).
The resulting transactions in Sage 50 UK&I will be:
a) a Purchase Invoice (as normal - DR Expense/Liability, CR Accounts Payable).
b) a Purchase Payment for that same Purchase Invoice (DR Accounts Payable, CR Payment Account).