Stacks are a great way to manage content that appears across multiple pages of your site. But managing the stacks themselves is not very intuitive. It's easy to add and delete stacks from the dashboard page, but there is no obvious way to change their names or change the order they're displayed in.
Under the hood, stacks are implemented as pages (that is, collections of blocks). Knowing this, you can deduce that stack names and display order could be managed in a similar fashion as any other page on your site -- via the site map!
Navigate to the "Full Sitemap" dashboard page, and click the "Options" link near the top-right of the window.
Click the "Show System Pages" checkbox to make various hidden pages appear.
Click on the little plus sign next to "Stacks" to expand its child pages (each child page is a stack)
To change a stack's name, click on its page in the list and choose "Properties" from the popup menu...
...and edit its name just like you would any other page.
To change the display order of the stacks, drag-and-drop the little icon next to the stack name (just like you would with any other page). Be careful not to move the stack outside of the parent "Stacks" page, though -- I have no idea what would happen but I bet it's not good!