In most cases you pay the skipper in person, in cash, when you meet on the day of check-in. Your booked quote shows what you pay online and what you pay at the marina, so check it for the skipper fee. If anything is unclear, ask your booking agent before you travel.
Is the skipper included in the charter price?
Usually not. The skipper's fee comes on top of the charter price, so budget for it separately. It depends on the length of the trip, the size of the boat and the skipper's experience.
Your skipper also needs meals on board and a place to sleep. See Do I need to provision the skipper/crew? and Where does the skipper or crew sleep?
Should I tip the skipper?
A tip is not mandatory, but it is customary at the end of a good trip. Skippers usually get the fee for one extra day as a tip. In the end it is up to you and how happy you are with the service.