How to I remove rotating banner & link?
Design and Skin Customization
Yes, if you are making changes to templates and then uploading those changes via FTP then your changes will be overwritten when you update the skin, if you are making changes via the ACP > Skins > YOURSKIN > Style and Templates sections, updates will NOT overwrite your changes.
If you are using a FTP client to upload your changes, you should really consider cloning the skin your going to make changes to so your modifications don't get overwritten after updating.
You can do so by going to your ACP > Tools > Developer Tools > Tools section and click the "Clone Skin" button.
Hope this helps!