qa-theme-base.php is a core file. Changing those is strongly discouraged, because the changes will be lost whenever you update Q2A. Instead override the respective methods by modifying an existing theme or creating a custom one.
Follow the method calls in head() and/or body() to find the particular method(s) that render the element(s) you want to modify and override those methods in your theme.
Alternatively, if you just need to insert a fixed HTML snippet in each page, you could do that under Administrative tools → Layout with one of the "Custom HTML" options.
