You will be fine. WHenever you rename the skin. Womanually remove any left over files with the same name that you just changed it from. Example Superskinv1 gets renamed to superduperskinv1. In the folder of the superduper skin, delete any non image files labeled superskinv1. You can build yourself a better template everytime you make a new skin as you are familiar with all the images. Diamond is missing some random coding as well.
The logoff buttons are controlled by the right pane image edge. You can't move the logoff buttons for Vista. Same with the search box. It's right side is set by the right pane image edge. It's all pretty screwy. Move hte buttons by manipulating the images. See my iSpire skin for example.
You can adjust the laft edge of the saerch bar under the bottom bar extra tab.