John to answer your question, yes you will use the extra holes in the smaller doubler plates to match drill through the spar onto the other larger doubler plates.
I have a tail kit from 2011 before these extra smaller doubler plates were added via a Van's SB a few years later so my spars didn't have the extra holes drilled in them. I don't know if they still come from the factory like that but if you have a new kit, then I'm guessing you still have to match drill those holes just like if you were complying with the SB after the fact.
Download SB 14-02-05 from Van's website. It will give you clearer instructions about adding these doublers than will the regular instructions. These parts are now incorporated into the empennage kits but you don't get the more detailed instructions like you do if you added them by doing this SB.
Look at my build log, there's plenty of pics in there of this part of the build.