Clarifying / adding some facts in...
PokeBalls
The recommended PokeBall for you to use is the Timer Ball. After 30 turns (I believe), the Timer Ball is statistically twice as strong as the Ultra Ball, and thus four times as strong as the ordinary PokeBall. If you can manage to stall Kyogre / Groudon, then the Timer Ball should really work for you. If you don't have the patience, resort to Ultra Balls.
Status
Inducing Sleep to the target is preferred over inducing Paralysis because sleep is proven to be statistically stronger. In fact, both Sleep and Freeze conditions are proven to be twice as strong as the Paralysis status condition. Make sure you have a sleep inducing move with you. Sleep can also be key to stalling your target out for the Timer Ball.
Health Points
You want to whittle down your target's HP as much as you can. Use a couple of harsh blows until you get it in yellow (or possibly red). The move False Swipe is highly recommended for this because False Swipe guarantees that it will never knock your opponent out. Note: This is a perfect reason why you don't inflict the target with HP draining status (like poison / burn).