6/9 is health/energy standard. It means you get allotted 6 hyper beam worth of health and 9 hyper beam worth of energy. 1 hyper beam is considered to be extreme damage. A pokemon can theoretically survive up to 6 fully charged Hyper Beam before it KOes, or it can use up to 9 Hyper Beam worth of energy before it faints from exhaustion.
4/6 cuts the length by some. This is used for leveling matches where one trainer might need to level up a pokemon. I have pokemon that are currently level 1 that need to participate in a match to increase their level to level 2. It goes by much faster, and I would not recommend it if you do not feel comfortable with the battling system just yet.