There are two ways to modify a theme: within the admin or using an FTP program.
To modify a theme within the admin:
Log into your CoreCommerce Admin Panel.
Hover over the Design tab and click on Advanced Options
Here you'll be able to edit the header and footer files, as well as the CSS files.
To modify a theme using FTP:
First you would log in via FTP. You can find your FTP login information in your admin under Account > FTP.
Once you log in via FTP, you will need to find the folder number of your theme. You can view the theme number by going to Design > View More Themes > My Theme in the CoreCommerce Admin Panel - the active theme number is on the top left. Look for the folder in FTP corresponding to your theme number (e.g. 00011-1).
In this folder you will see two folders: "design" and "templates". In the "templates" folder you will be able to access the header and footer files, as well as the widget sidebar and top navigation files. You will need to edit the header.html and footer.html to edit the theme design. The secure ones are when you are behind an SSL (e.g. My Account or the Checkout page) and are secure.header.html and secure.footer.html. To access the CSS files, click on the "design" folder, then you will see a folder called "css"
Note: CSS files that are uploaded via FTP should be applied immediately. However, for HTML files, you will need to go into the admin and choose to publish them before the changes will display.
Below is a video that shows you where to edit your design.