Haha, wow. I didn't even manage to get 500,000,000. I have yet to try it again.
Scoring in Novice mode and 1.5 Original:
If you look closely, you'll notice that your counter at the top of the screen changes from green to blue. When it's green, use your C shot, and everything you kill or destroy will yield large amber items. Using your A shot when it's green will only give you small ones.
The opposite goes for when the counter is blue. Use your A shot at that time, and avoid using your C shot.
Do keep in mind that your C shot is significantly weaker than your A shot, so you may not kill midbosses properly if you only use it with a green counter. The trick to this is to use your A shot just until it's almost dead, then switch to the C shot to finish it off.