I understand that a percentage is saying, how many parts there are out of 100. So 65% represents 65 parts of out 100 possible parts.
One thing that I can't get my head around, or I am over thinking, is that if we have something such as $9/12$ and I wish to know what percentage those 9 parts out of the 12 take up, what exactly am I doing? Am I saying that if the 12 parts were infact 100 parts, how much would the 9 parts now take up?
The choice of 100 is rather arbitrary. If we had six fingers on each hand, we'd probably use pergrossages rather than percentages. Then your 9 twelfths would be 108 pergrossage.
Perhaps the most natural thing is parts of a unit, that is, parts of 1. One divided by 12 is approximately 0.083333, periodic but non-terminating in decimal. Multiply that by 9 and you should get 0.75, assuming no loss in calculating precision.
If that looks like 75%, it's only because we use the decimal system. Try this in Wolfram Alpha:
3/4 in duodecimalThen try108 in duodecimal