Does the second region have it's own pokedex or do the 2 regions share?
And also do you keep all of your Pokemon from the first region when you go to the second. Visa, versa.
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Before you go to Kanto you're given a National PokeDex, which can obtain data on all 252 Pokemon (and the following 235 from Hoenn and Sinnoh, provided you trade).
Yes, you can keep them.
There's not two Pokedexes. After Defeating the Elite Four, Professor Oak will be in the Olivine Harbor Building, and he'll give you the National Pokedex before you get on the SS Aqua. (The National Pokedex has all 493 Pokemon from every Generation, though to get info on them, you need to trade from Diamond/Pearl/Platinum and use Pal Park in D/P/Pt/HG/SS to get Pokemon off of Ruby/Sapphire/Emerald)
For more questions for Pokemon Soul Silver check out the question page where you can search or ask your own question.