On the first point, the rules state that you need to buy an appropriate single/return for the additional journey:
From ATOCs» Excess Fares Procedure:
Over-riding (travelling beyond the destination on the ticket)
Except for Season-ticket holders, a customer travelling beyond the destination of the ticket will be required to pay an Excess fare for the difference in price between the ticket held and the appropriate Single or Return fare, available for immediate travel, for the complete journey from the originating station to the final destination. Alternatively, if cheaper the appropriate Single or Return fare available for immediate travel, for the additional journey may be charged.
Season ticket holders need to pay the appropriate Single or Return fare for the additional journey.
If there is an opportunity to do so you should buy this additional fare before boarding. So if the ticket cabin is open at Nailsea and Backwell then buy from there. If it's not open then fine to buy on board (or at destination if no opportunity onboard).
As regards your second query, if you have a season ticket from Nailsea and Backwell to Stapleton Road then it is valid for any intermediate journey(s) between those two stations.
TOP TIP: Buy the season Nailsea & Backwell to Clifton Down for extra journey opportunities. Still the same price as to Stapleton Road!
Now you just need to work out whether to buy the cheaper season to Bedminster (^67.20 month, ^700 year) with the occasional additional fare or the more expensive one to Clifton Down (^75.70 month ^788 year). That'll depend how many additional journeys you plan to make if you buy the former.