So in my quest of learning this software I've been sent a file with a large header. some of the pins require high currents between relatively small pins, I noticed between layers some of the through holes do not have pads around them. I've tried to play with the pad stack editor, but it seems I can't recreate this properly. I attached the following as an example. This is layer 3. Top row of pins have pads, bottom don't. 
I shall continue playing, however if anyone has any advice I'd be grateful!