You can renumber the annotations, by right-clicking and using Footnotes->Increment/Decrement Footnote. There are also toolbar buttons for this in the Object toolbar (View->Toolbars->Object). If you want to renumber all of the element top down, left to right, you can use Wireframe->Renumber All Footnotes and it will do it's best to ...

There is not a way to do this currently. We've had some requests to be able to change the size of them as well. Thank you.

Can you change the footnote standard (yellow with black font) appearance?