When a confirmation email goes to the customer/vendor

The confirmation email goes to the customer before the SagePay section (payment) has been completed? It should really go after when the payment has been confirmed and the order confirmed - anyone know how to do this please? Many thanks!

There're two emails sent to a customer:
1) Order placed
2) Order completed

If you would like to remove "order placed" email please open OrderManager.PlaceOrder() method and remove the following code:

int orderPlacedStoreOwnerNotificationQueuedEmailID = MessageManager.SendOrderPlacedStoreOwnerNotification(order, LocalizationManager.DefaultAdminLanguage.LanguageID);
InsertOrderNote(OrderID, string.Format("\"Order placed\" email (to store owner) has been queued. Queued email identifier: {0}.", orderPlacedStoreOwnerNotificationQueuedEmailID), DateTime.Now);

is there any other way to remove from nosource site?

No.  Because you need to alter a .cs and any change to a .cs file requires you recompile.