After rereading R.C. Anderson's article "The First Dutch War in the Mediterranean", I finally realized that Van Galen's squadron (or fleet) was anchored right outside the harbor of Livorno. I'm not sure where they were anchored, in relation to the harbor mouth. In my Privateers Bounty scenario, I placed them North of the harbor entrance.
Interestingly enough, when I ran the simulator, the Madonna della Vigna was disabled relatively near the shore. In the actual battle, she was the only Dutch loss, and had been run ashore.