What search box gets rendered depends on the search settings for the site collection (ie: with scope dropdowns or without). If you want to standardize the style of the search box, you'll also have to standardize that configuration, or make sure you rebrand both search controls.
While it's not a best practice (as they can be changed by Service Packs or CUs), you shouldn't edit the out of the box control templates. In some scenarios (like changing the help icon or other 14 hive icons), that's the only way I know how to do it. Map the applicable folder in your Visual Studio solution and push your own, rebranded copy of the file as part of your activation code.
In scenarios where you have to do this, I like to also store an original of the OOTB file in my solution, and set deactivate code to revert back to the original. This way if a solution is deactivated and retracted, you're back to OOTB SharePoint.
One other important thing to note, is that once you change that feature, control template, or 14 hive asset, you're now going to affect everything on the environment. You either need to duplicate/create your own version, or find another approach if you want to have sites where that search box doesn't look the same.
As an example, extranet branding is typically a little (or drastically) different from intranet branding. If you were to spin up a new extranet site and you've overridden the native search feature styling, that new extranet site will be forced to use the same.
I guess the first question is what changes have you made to make it "pretty" that you couldn't have done via CSS, or a custom control template vs. modifying the OOTB search feature.