Re: Dumb question...
Not a dumb question. As someone who was briefly CFO for a very small organisation, you use HMRC tools or something like Quickbooks (definitely not a recommendation!) to calculate their tax and NI, providing you’ve correctly identified their NI status (not so easy as you think). You then submit that electronically and pay what HMRC says you owe to them. Much the same for pension contributions. You should be able to ask to see this if you had a dispute.