To add to Jay's answer, here are some more specifics on the actual way the V_in, 5V, and 3.3V voltages are generated. Again, since you did not specifically say which board you are using, I will operate under the assumption that you are using the good old Arduino Uno. You can refer to the following as I go:
V_in is the voltage that you input to the board through either the Power Port or the USB connector. You made reference to this being 9V, and this is usually the case if you are plugging a 9V battery into the barrel connector like so:
This V_in voltage goes into the Voltage Regulator in the diagram, and you can look up the datasheet of that part if you would like to learn more about the voltage limits, etc. A similar part is LM7805 if you want to look at how that works:
The output of that voltage regulator is what produces the 5V which is available at the 5V pin. The amount of current you can pull out of this again corresponds to the values outlined in the datasheet of the voltage regulator.
Finally, the 3.3V is actually produced by the part labeled USB Interface Chip. Here is the datasheet for the part:
I'll save you some digging, the max current you can pull from this pin is available in the first box on page 8 (50 mA).
So to answer your question, as long as you do not exceed these current limits, or get too close to them (thereby disrupting to Arduino's power source), you should be able to use them as you please.