We have upgraded to the newest version of the ReBoot Template. How do we restore all of our customizations, settings, etc after uploading the new files?
Assuming you made a backup of your skin/reboot folder before the upgrade, you can trace/redo your customisations by using a file comparison tool such as KDIFF
or Beyond Compare
If you have applied the new SQL patch, then you'll need to redo your settings.
When you start customising, it's your responsibility to keep track of changes made to the templates, make appropriate backups etc.