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Tomer,
You cannot change the quantities arbitrarily. You will need to change the targeted capacitance value. You can edit the capacitor limits and you will get a different selection of capacitors (some in parallel) to hit that new target.
If you want to control all aspects of the device, you can create a custom part and put the quantities in parallel into your custom component.
If you are creating a custom component for a capacitor, you will have to take care of the derating and ESR values.
WEBENCH uses the following derating method when the design is generated. It finds the required output capacitance, then picks values that will derate to that value and chooses that value for the output capacitor. There are other rules involved as well. Here is a post showing the derating curve used.
The quantity change and limited ranges are in the tool to make sure that the design is robust for the requirements specified. Once you edit these fields, you will need to make sure that the design will still meet your requirements. There are many rules built into each device that help the tool create the design. WEBENCH is trying to make sure that the device will work across all of the specified requirements so it may be more conservative that you wish.
I hope this information helps.