Today I spent a good portion of my time trying to figure out how to configure a CQWP (though, this applies to all WPs) to ensure the top web part in the given zone showed up on top. For the life of me, I couldn't find the setting in SPD that corresponded to Zone Index and every time I used the page layout the new created page flipped the web parts and put the top one on the bottom and vice versa. How did I solve it? I deleted the bottom one and re-added it using the logic that since it had been the first one added was the reason it was showing up first. This really isn't a precise means of governing proper page layout! Please tell me I missed something.