changing theme on custom WordPress site

I was just hired to work on a WordPress site. I have more experience on Joomla, but limited knowledge with WordPress.

The site that was build was a customer site using the WordPress platform. But what I noticed is the last developer either removed or hidden the function to upload themes and plugins. The theme they are using is a custom theme, but my boss wants it changed because it doesn’t really work. Also, I need to upload a shopping cart pluggin and there is not a function on the backend to do this. I know there must be a simple what to do this. Would I just add the files via FTP? How can I add these functions?