As usual with our apps, the scripting support is natural. Once you install Power Custom Fields Premium™, you can access the custom fields via the usual syntax: customfield_<id>.
The value of the field is always an array of KPOption representing the selected options in the field.
Example
//simple example on how to access (get/set) Power Custom Fields PRO fields
//we assume we have an issue context here
KPOption [] options = customfield_12345;
if(size(options) > 0) {
runnerLog("First option id = " + options[0].value + " and the label is :" + options[0].label);
}
//we'll assume this is a multi-select field, because otherwise it will not work
KPOption nopt;
nopt.label = "Extra topping";
nopt.value = "99";
options += nopt;
customfield_12345 = options; //here's the set