Your statements are a little confusing, so let me first make sure we share some definitions so that we are speaking about the same thing.
If your site is built with Joomla (which is a Content Management System), then you would need use the Joomla application in order to work on your website. When you say "site builder" - that is a totally SEPARATE program that has nothing to do with Joomla. You cannot use the Builder in order to work on your website (unless Register.com is using a Builder program that can load Joomla websites - and we're not familiar with that here at Web Hosting Hub).
Joomla is FREE. If your website is built with Joomla, then ufortunately, you will need to log into Joomla in order to work with your website.
Cpanel is an interface used to provide a suite of tools that can access the hosting server (where your website lives). If you're paying for your hosting, I'm not sure why you would be paying to update the content of your website (unless you're paying someone else to do so). As long as you're paying for your hosting server, you can always reach your website files using the Cpanel interface (File Manager) OR the FTP client - Filezilla. You said that you're using Filezilla, so instead of using the Cpanel interface you're using the FTP client to directly access your website files. This is not a web-based interface, it uses FTP.
Additionally (as you have pointed out), Joomla has it's own login, so it sounds like you're locked out of the Joomla installation.
I can't see your website files since it's not hosted with us. I do not understand how you're hosting your website, but if you own the website and you're paying for the hosting, then you should be able to login to change your files at any time. There should be no need to bypass a login - unless you're not paying for the actual hosting account. If that's the case, then you need to get your own account, or speak with the person with whom you're hosting your website. We couldn't begin to bypass the website without direct access to the database. If you have lost your password, we DO have an article that shows how to RECOVER the password for Joomla, but again, you will need direct access to the website files using the Cpanel. Here's the article: Resetting the Joomla Password
If you wish to host the website on Web Hosting Hub, we can help you get setup, but the website development and operation is up to you. We provide a lot help through our support systems, but we can not bring those resources to bear on your website unless you have an account with us.
Apologies for the frustration and difficulties you are having working with your website.
If you have any further questions, please contact technical support or leave a comment at the bottom of the page.
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