When baking but bread in 12 inch logs, do they need to be in a 13x9 pan or can they be baked on a cookie sheet?

A cookie sheet should be fine. In fact, I would think that would be better, as the hot air will circulate more evenly around the logs. Keep an eye on them, though, and rotate the cookie sheet once or twice if necessary, i.e., if you have hot spots in your oven and they are not baking evenly. ;o)