John's answer basically covers it - I presume the developer calculates the percentages, and they are included on the master deed for the entire property when registered at the land registry.
On a side note, I purchased an off-plan property some years ago, and noticed that the amount the administrator asked me to pay represented slightly more than my percentage of the total budget. On querying this, the admin told me he had discovered that the total cuotas came to 99.42% only, so the annual budget had to be adjusted slightly, and my resulting payment was slightly more accordingly! So, just for the sake of contradicting John, All the coefficients do not always add up to 100% !!!
Presumably the descrepancy on the deeds came about from rounding up the coefficients. It could only happen in Spain!