Mike
Randy is correct - if the pen is constructed in two sections, then it makes a lot of sense to cut the blank in half BEFORE drilling the hole. There's no sense in making the job any more difficult than it needs to be.
But one additional piece of advice - before cutting the blank, put some marks on the side of the blank so that you can tell later which are the ends of the blank that were cut. Then, if you have a dominant grain pattern, it will be much easier to match grain across the middle of the finished pen.
But also, when you drill, always drill from that cut end. The drill will be reasonably close to centered at the end where the bit enters the wood, but may wander off axis as it goes deeper. Drilling from the cut end (which will eventually be the center of the assembled pen) will assure that the hole in the blanks are centered at the point where the grain pattern will be matched, and improve the quality of the grain match.