Sky Pillar Bonus Level
To get to the Sky Pillar Bonus Level, you have
to go to the Dusclops Bonus Level, beat it, then
beat Kyorge's/Groudon's Bonus Level, do the same
thing agian (Dusclops Level, Kyorge's/Groudon's
Level), beat those two again and then you'll met
Rayquaza in the Sky Pillar Bonus Level!
Other Way To Get Extra Ball
Even after you buy an extra ball, you can still
get one whenever there's one in slot (it's easier
to get in Sapphire, since the Zigzagoon can stop
the slot where you want it).
Latios(Ruby) and Latias(Sapphire) are not found
in any specific location. They will just pop up
at random, no matter where you are. They rarely
appear, though, so try not to play just to find
one of them (you most likely won't find them).
One Extra Ball Per Play
Whenever the mart is open, you can buy an extra
ball for 99 coins, but if you buy that, you won't
be able to buy another one, for it will say it's
sold out, so you can only buy one ball per play.
To catch Kyogre/Groudon you have to beat them
twice in the bonus level. In ruby field beat the
kekcleon bonus. Then evolve one pokemon and catch
a pokemon. Go to the Groudon level and beat it.
Do this twice to catch Groudon. For the saphire
field, beat the dusclops bonus level. Then evolve
a pokemon and catch one. Go to the Kyogre bonus
level and beat it. Do that twice and you will
have Kyogre and Groudon.