You can't find Helix fossil in soul silver, so you can't obtain Omanyte (except for trading from another game), you can only at heart gold. The one you can get instead is Dome fossil, for him to give you Kabuto. Old amber is the one for Aerodactyl, that one you can get at both games, by rock-smashing at Ruins of Alph indeed; and I think you can get another Aerodactyl by trading a Chansey with the lady standing in the grass at the north of Pokemondb.net/location/kanto-route-14, but there seems to be no limit of old ambers to find at Ruins of Alph. Besides the Magnet train, you have the choice of flying too; when it's between regions, you just have to land at Victory road or the Elite four building, and then your destination; when you're standing outdoors at those two points, or Route 26 (the one directly south of them), you can fly to either of both regions.