Think of the condenser as a closed water pressure tank. Suppose the tank holds 2 gallons and you force one gallon of water into it. Pressure inside will rise to a certain amount. Now, lets say the tank size holds 3 gallons and you force the same one gallon of water into it. Pressure inside will rise to a lesser amount than before.
Now as applied to condensers, if you force a certain amount of electricity into it, pressure inside will rise to a certain amount. In this example, "pressure" is called "Volts". A larger condenser capacity will result in lower Voltage buildup, assuming the same amount of electricity.
It matters because it determines the voltage of the electricity as it discharges back out through the coil when the points break. That reversal back through the coil is part of what creates a spark at the plug.