PokéBase - Pokémon Q&A
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You can catch Groudon/Kyogre (depending on your game, Groudon=SS Kyorge=HG) when you have the Red Orb (for Groudon) or the Blue Orb (For Kyorge)
For you, since you have Soul Silver, you'll be able to catch Groudon.
If you have a Kyorge that was caught at the Embedded Tower in Heart Gold, Professor Oak will give you a Jade Orb to catch Rayquazza!
Here is a video to help you.