As with all stationary pkmn, the spread or frame is selected when the battle starts. Somewhere in a post by Hozu, Hozu stated that the once the animation start until the battle beings, approx 256 frames will have passed.
Steps you need to take
1. Save one step from Groudon to where the animation will start when you move to the left once.
2. Find a spread and us eontimer.
3. Start the timer and move once.
*Note the game will say "This blue/red orb being to glow."
4. Once your timer hit zero hit A to exit the "orb message, which will being the animation."
5. Capture Groudon, update the timer based on what spread you hit and raise and repeat until you get the pokemon.
Thanks you two.The on-site R/S guide has frame times for Groudon.
I tried it on an Emulator and it seems that the spread is selected after I press A when the message comes- "Player's Red/Blue Orb began to glow"