Question regarding input and output voltage

I don't think you've quite understood the difference between 'voltage' and 'current'. You should probably watch some youtube footage, there are plenty of movies explaining the difference.

If a led needs 3.3V and uses 25mA current, adding more leds together in parallel (so all cathodes together, and all anodes together, basically laying all leds next to each other and solder all 'sides A' and 'sides B' together), the voltage needed will not change. You will still need to supply 3.3V, not more. "3.3 x 3 = 9.9" doesn't make sense here.The only thing that will increase is the current. 3 leds will make 3x25mA = 75mA.

You always need to be careful not to draw to much current (mA) on one pin, I believe on Arduino it's maximum 40mA per pin, and not more than 150mA all together.