Re: bunk height adjustment
It depends on the boat. There is no "only" way for all boats.
Boston Whalers, tinnys with reinforced keel and any other boat that has its strength in the keel should rest on keel rollers with the bunks keeping it balanced. These boats are best trailered on keel roller trailers rather than Easy Loader type roller trailers (though Easy Loaders are a lot easier to load).
Boats with stringers providing the bottom strength should rest on bunks with rollers centering it for loading. These boats do well on Easy Loader all roller trailers.