To use a custom favicon for your Ghost blog:
Copy your favicon.ico file to the /assets folder inside your theme folder (/blog/content/themes/themeName/assets).
Open the default.hbs file of your theme
On line ~15 replace
<link rel="shortcut icon" href="{{asset "favicon.ico"}}">
with
<link rel="shortcut icon" href="{{asset "/favicon.ico"}}">
Save the default.hbs file, and refresh your blog.
That's really all there is to it. Ghost uses this default favicon, unless you specify your own.