Upgrading is usually and should be a fairly easy task. I'm using the term "purchased style" in reference to which style you own and are actually upgrade(Core/Fusion Gamer/Apex ect...)
Step 1.) Backup your style first
Backing up your style prior to upgrading is always good practice. In case something does go wrong you can simply re-import your backed up style. Check out this guide to backup your style.
Step 2.) Update your XenForo
We release style updates along-side XenForo updates normally. To make sure your templates are updated properly you need to update your XenForo before updating the style.
Step 3.) Upload the new XenBase folder
Upload the new /xenbase/ folder inside the included /styles/ folder, we'll inform you if you need to upload the purchased style folder(usually changes aren't done to that one at all)
Step 4.) Import and overwrite XenBase
Import the new XenBase XML and choose to overwrite your existing XenBase style.
Step 5.) Import and overwrite the "purchased style"
Import the new "Purchased Style" XML and choose to overwrite your existing "Purchased Style".
You'll leave your child style alone as all of the fixes/improvements trickle down automatically to your child style.
All of your edits will go inside your child style
If you see something off... don't panic! Periodically settings can get turned on/off by default so if something seems a little off on the style feel free to submit a support ticket or post on the forums.
If something is really off you can simply revert back to your pre-upgrade style by re-importing the XenBase, Purchased Style and your child style in that order and overwrite. It will take you back to your version prior to upgrading until you/we can figure out the problem.