Allen Dailey it sounds like you have the pages listed across the top of your site as header links, is that correct?
If yes, you can reorder those links via drag-and-drop by opening the site's layout editor and selecting the following...
1. Open Customize Panel
2. Select "Header"
3. Select "Menu" accordion
4. Drag-and-drop menu link pills in order desired
The pages list in the layout editor is just a general list of linked pages and doesn't directly tie to any navigation element or layout card in the site.
Hope this helps.