snippets rarely working

I have a WP 3.5 multisite setup where buddypress is on the main site.
I need to set up the main site so that subsites appear to be served up from the main site.

However, most of the snippets I find don’t seem to work and I am wondering if it is because of how my topology is set up.

For example, since the main site is a BP site, it’s theme and functions.php file is not at the top of the hierarchy, it is
/wp-content/plugins/buddypress/bp-themes/bp-default/functions.php.

I am assuming this is why most snippets are not working network wide.
Do I need to set up another sub site, then make that one the BP site and main site?

By the way, I am using a plugin called Snippets so that I don’t lose all of my customization when there are updates.

I’m a bit confused and sure could use a little input.

Thanks.