do you need to use the center tap to get 1/2 the output voltage on the secondary side? if not, just wire nut the center tap and tuck it out of the way.
for example, if you have primary at mains, and secondaries at 12v, if you use the center tap and one secondary, you will get 6v. so if your goal is to get the most out of the secondaries, just don't use the centertap.
someone please correct me if i'm wrong.