Can you use the features module to replace existing functionality
Yes, you can. You can install features, then export all the things you want to change. Install the feature on a copy of the site you are working on, and export again, after you made the changes. (and reinstall again to that copy site, until you are satisfied).

Then copy your feature to your production site, enable, and revert the feature (revert in this case means, making sure the feature behaves like defined in the feature, hence upgrading).

Good luck!