starpeices, and big pearls, do i just sell them? or do i need them for something?
Sell them, the only purpose for them is to get money.
where is that guy who takes your shards?
He's in a house to the west of Mossdeep City. Go to the far western (left) side of the island, down the watery part where all the trees are. Surf and head directly left and you should see or run into a house on a sand bar.
how and why do i use my soot sack? (lol)
To fill it up, you simply run over the sooty grass on Route 113. Every step through the sooty grass gives you 1 more "unit" of soot. You'll eventually have to leave the route and come back to replenish the soot, since you only get more if you run over the grass when its gray, and once you run over it once it'll turn green. Then you take it to the glass blower guy and he'll make you stuff based on how much you have.
i just came to the part in Emerald when Rayaquaza (did i spell that right?) saves the day and Groudon and Kyougre flee. Do i have to seek them out and capture them? will i be able to capture them with ultra balls?
You can seek them out, yes. Its not required, however. They are quite high-leveled (level 70 I believe), so if your not using a Master Ball you'll have to train for quite a while longer if you want to try and catch them. But you can capture them with Ultra Balls, it'll just take a long time and be quite annoying, as it is with most legendaries.
is it possible to trade pokemon from my yellow game to my silver to ruby to emerald?
No, the advanced generation (Emerald, Ruby, Sapphire, FireRed and LeafGreen) are not compatible with the older games. A lot of things changed between the advanced gen and the colored/metal gens (the way stats are calculated among other things), so they couldn't keep backwards trading capabilty. The good news, however, is that when Diamond and Pearl are released (the new DS pokemon games) you WILL be able to trade with the advanced gen games.