FeedWrangler is a utility for creating and editing custom feeds.
The feed will take precedence.
Once you create a new feed in the Feed Wrangler interface, you can create a corresponding template file in your current theme to customize your newly created feed. The admin interface will tell you the file name to use.
If you want to start off with one of the default templates -- let's say RSS2 -- just copy and paste the code from
/wp-includes/wp-rss2.php in older versions of WordPress) into the new theme file and make the changes and additions you see fit.
On a Mac, I like using Firefox with the "Feeds" option set to "Show me a preview and ask me which Feed Reader to use". When you access your feed in Firefox, you have to clear the cache as you reload (COMMAND + SHIFT + R) -- otherwise you might have trouble seeing your changes. Viewing the source of that preview page will give you the raw feed source. Once the source looks fine, it's a good idea to drop the feed in an actual feed reader and see how it responds. Also, don't forget about Feed Validator.
If you're using version .1 of Feed Wrangler, you'll need to upgrade Feed Wrangler BEFORE upgrading your WordPress to 2.6.