I would recommend doing a little research on how Joomla works. This might be a place to begin, and other resources can be found here. A Google search might also give you some answers.
Basically, you manage a Joomla site through the admin area (http://example.com/administrator), and if you have Joomla 3.x or above you can also edit the template from the admin area.
In addition, you can usually make adjustments to the template from the Joomla template manager (Extensions -> Template Manager -> select the name of your active template). Depending on your template, you should be able to change colors, logo, and other parameters there.
You can absolutely edit files through FTP, but it's highly recommended to avoid editing core files (both Joomla and extensions), as these might be overridden if you update Joomla (and you should ALWAYS keep Joomla up to date). You can edit your template files, and if you need other modifications to Joomla or some of your extensions you can use a template overrides. This is basically a way of adding
.php files to your template folder that will be used by Joomla instead of the core files.
If you're stuck with anything, or have a questions, you're more than welcome to ask your questions here, and you'll almost certainly get answers.
Good luck :)