Upgrade Best Practices From 4.1.2 To 4.1.x

If you have in place a fully operational store with some third party add ons from reknowned CS-Cart partners and if you have custom skin installed. What would be the best practice to upgrade your store. I presume not the auto - install functionality that is now prompting me to upgrade from 4.1.2 to 4.1.3

Kind regards