Hi Claudia,
That's a beautiful theme!
I am attaching a document that explains how a custom theme plugin is usually installed, and how the files and directories in the custom theme are typically organized. It should give you some guidance on where to look, and it includes a number of links to other theme development resources we have.
In terms of updating links and shortcuts - it will depend on how the theme is built, but if they are elements that are normally part of AtoM (such as the Browse menu links, etc), I would first try modifying them via Admin > Menus. Sometimes developers will hard-code the custom homepage links, but a better method is to reuse the existing code and use the theme just to style them differently, as this allows users to make modifications to the links via AtoM's settings. See:
If this change doesn't work (or the links you want to modify are part of the custom theme only), then you will need to open the relevant file in the plugin directory and modify it using a text editor.
If the links are in the header or footer, then you will probably want to look for a file called _header.php or _footer.php, which is normally found in a subdirectory called modules/staticpage/templates inside the custom theme plugin. If they are links right on the homepage, look for a file called homeSuccess.php in the same place.
If you are trying to change the look of the links (for example, change the color), then you should look for relevant CSS rules added to the custom.less file, usually found in css/less inside the plugin.
I hope this helps!