let me make sure. Is your problem that you want to fill extension first ?

If yes, i suggest your change your find targets code, a simple change is

const target = targets[targets.length - 1]; // take the last target, it must not be spawn

and then

if (creep.transfer(target, RESOURCE_ENERGY) === ERR_NOT_IN_RANGE) {
  creep.moveTo(target);
}

I don't suggest you transfer energy from spawn to controller, because your spawn maybe has not enough energy to respawn died creeps.

For beginners , The tutorial role.upgrader code is the best code to upgrade controller, if it doesn't meet your needs, it's time to rebuild your code .