I assume that the travel into Waterloo would be for the days when you need to go to Ealing Broadway.
On days when you to Shepherds Bush, I assume that you plan to change at Clapham Junction.
One alternative for Ealing Broadway days would be to go to Shepherds Bush and then use the Central Line from Shepherds Bush to Ealing Broadway, which is already covered by your travelcard.
Otherwise, if you prefer to go via Waterloo and Paddington, you would need to alight at Clapham Junction and touch in with PAYG oyster/contactless before continuing to Waterloo.
Or you could before departing Guildford buy a Clapham Junction-Ealing Broadway paper ticket: as you would be combining that with a season ticket, you could then (condition 19 of the National Rail Conditions of Carriage) travel into Waterloo without alighting at Clapham Junction, and even do so on a train that doesn't stop at Clapham Junction.
Edit: I should add that there is a "not via London" season ticket, a bit cheaper than the one to Zones 2 to 6, for the Guildford-Clapham Junction-Shepherds Bush route, although that would not give validity off-route or on buses or tubes. With that ticket, you would need to use PAYG oyster/contactless for Shepherds Bush-Ealing Broadway on the central line.