Short answer: The 6% does not mean 6% of the total impedance of the system, but rather 6% of the value of “base impedance.” Longer answer follows.
Yea, I am afraid you are missing the fundamental concepts here. There are formulas that relate a single components voltage, current, apparent power, and resistance to each other. Given any two of these values, you can calculate the other two. Similarly, within the per unit system, there are the concepts of base voltage, base current, base power, and base resistance. Here again, given any two base values, you can calculate the other two base values.
If the “base voltage” is assigned to be 480 volts, and if a given component has a voltage across it of 10%, or equivalently 0.1 per unit voltage, then the voltage across that item is 48 volts. So if the manufacturer says that an item has an impedance of 6%, then in order to convert that to ohms you need to know the base impedance.
It is common practice to assign base values to voltage and VA. Starting, for example, at a utility transformer that feeds a building, with a rated value of 500 KVA and a rated secondary voltage of 480, it would be common practice to assign the base voltage as 480 volts and the base apparent power as 500 KVA. Thus the transformer would have values of 1.0 per unit voltage and 1.0 per unit apparent power.
Back to your motor. You know the motor’s rated voltage and KVA, so we would presume the manufacturer would have used those values as the base values. You need to calculate the base impedance. My text book is not immediately available, so I can’t tell you the formula right now. Perhaps someone else can give you that. Once you calculate the base impedance, multiply that value to 6% (i.e., by 0.06), and you will have the impedance in ohms.