Hi I made my VAT3 return for Sep/Oct through your software and also made the payment on 15th Nov. However, it still seems to be showing up in my ‘to-do’ list. how do I change this?

You need to mark it as paid. ROS don’t let you integrate with them so we don’t know if you’ve paid it unless you tell us. Just click on the todo, click the link in the todo and then click Mark as Paid 
See the image below.