In general terms there would be a cover note with a recommendation to the Prime Minister saying, here's a batch of orders in council or a specific order in council that you need to take a decision on.
The Prime Minister has a particular role in appointments and a particular role in changes to the machinery of government—the pulling apart and and putting back together of government organizations.
Typically there would be a note from PCO giving a recommendation or options and asking for his agreement, and these would usually come back from the Prime Minister with an initial okay or some kind of indication, or they would sit for a while before they came back.
There is a document management system that logs every single note the PCO sends to the Prime Minister and every one that comes back.