Hi, i am new to caravanning too, having just bought my first one last year. It certainly is an experience finding your way around things!
A pup tent is basically a small one or two man tent, usually about 6ft long and about 4ft wide. You probably could erect it inside an awning for extra sleeping space but it would be a tight squeeze because of all the guy ropes!
With regard to the awning annexe, as long as you tell the site that you require space for an awning then you will have no problems with the annexe. Some sites will charge extra for the awning (usually a couple of pounds per night).
When you book a site, the charge usually covers the caravan and up to two people. Anyone over the two will pay an additional charge.
Charges vary from site to site and it always pays to ask when booking. You will usually have to pay extra for the electric hook up, sometimes if you take a dog with you........it can be a bit of a minefield so do ask these questions!
John