We woke up early and watched as our ship first entered the harbor--it's quite a ways from their to the town of Kotor, but the bay itself is beautiful and we were glad to spend the couple of hours on deck as we went through. Don't know what time your ship is arriving, but we got there just as the sun started to come up from behind the mountains--nice photo op.
Once we got to Kotor, we walked a bit up the old town walls, then just walked around the old town. Had a good lunch at a cafe located on one of the main squares and had a sandwich made with prsut and sour cream--I would recommend ordering something similar if you find it, as it was delicious! We did not use a guide, just followed the info provided by our cruise line and what was in the RS book.