Go defeat the elite four again and all non caught legendary Pokemon reset
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find groudon at the magma cavren and kyogre at marinea cave
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yes. After you get the silver feather for Lugia and rainbow wing for Ho-oh. in Soul-Silver you find Lugia first and in heart gold you find Ho-Oh first. You cannot get BOTH Kyogre and Groudon though.
After beating the Elite Four and champion, you go to the Weather Institute outside Fortree City. Talk to the man inside and he'll tell you that there is an unusual amount of rain somewhere in the region. You travel there (you'll need to surf to find it), find a dark spot in the water that wasn't there before, use dive, and you'll enter Marine Cave. That's where Kyogre is. Once you either catch or defeat Kyogre, go back to the Weather Institute and talk to the man again. He'll describe somewhere with an unusual amount of sunlight. You travel to that area, find a cave entrance that wasn't there before and enter Terra Cave, where you can battle Groudon.
It means they cannot be found again unless you saved before you fought them then you can just restart. If you saved after you killed them then you can't find them again, so you have to restart the game if you want to catch them.