Unfortunately I cant find the online S&S rule book but if I remember correctly, when you defeated a ship during a scenario you could seize it and use it for the rest of the scenario. Now there is new rules in intro for season 5 regarding seized ships. My questions is do these rules overwrite OR or they additional rules for seizing ships?
RULES: SEIZED SHIPS
When you seize a ship, record it on your Chronicle Sheet. At
the start of a scenario, you may cross off a ship you have
seized to use that ship instead of the Feathered Devil.
They are in addition. If you seize a ship that blocks Structural damage, you might want to bring it out for a scenario with lots of structural damage, for instance.
[...] but if I remember correctly, when you defeated a ship during a scenario you could seize it and use it for the rest of the scenario.
I'm afraid you can't just seize any ship you defeat, as per the rulebook; you need to have some kind of power that allows you to seize a ship. Most notably, the 'Enemy Ship' barrier henchman states that you summon and encounter a ship, and you may seize it if defeated. If some other effect causes you to encounter a ship and it doesn't mention anything about seizing, then you can't seize it; simple as that.
That does mean that actually getting opportunities to seize ships are pretty rare; you need to be in the right scenario, generally.
Very true.
There is eventually a scenario reward to help you out with a lot more opportunities.