Upgrading modules and preserving overriden features Workflow

Noobie to features question.
First if someone could just point me to some documentation about this (I can't seem to find and/or understand what I am reading.
I have a D7 dev site with Commons and OG. I want to upgrade to the latest Commons. The instructions for upgrading say to revert all overridden features after updating. Make sense. Obviously though I want to preserve my overridden features.
So I:

1. Update the overridden feature -- but do I want to push my overrides to the database or to a custom module folder like site/all/modules/custom/your-feature as described here?
2. So now that it is updated no need to revert....but couldn't Commons make changes that would be incompatible with my overrides?

Or do I:

1. export my overrides to a module
2. update Commons
3. revert overridden features
4. install (import my overrides/fork)?

This makes it sound like a fork of the feature...?
Any guidance would be welcome.