When a skin is updated in the Marketplace, its files are replaced. A clone is your own copy of a skin, under a new name. Updates never touch it, so it's the safe place for your changes.
Clone the skin before you change its templates, even for small changes.
On a new site, run an Integrity Check first (ACP > Modules > Core > System Core > Tools > Integrity Check). The clone then remembers which skin it came from. Without that, the Compare highlighting and Create A New Template In This Skin don't work for the clone. See Keeping a Cloned Skin Up to Date.
xxMySkin.You'll see "The xxMySkin skin has been cloned from the jrElastic2 skin", on the new skin's Info tab. Check Set As Active Skin and save to use it.
The clone gets the skin's files and your changes to it:
Edit its templates on the Templates tab (Using the Template Editor), or edit the files in skins/xxMySkin with your own editor. To bring later updates of the original skin into your clone, see Keeping a Cloned Skin Up to Date.