Default blog values via add_site_option/get_site_option

hello

I have never before needed to deploy or use MU. Just recently, a client needed a multi-site product developed, and when I found out that 3.0 was merging MU with regular WP I was pretty happy. Got 3.0b2 installed and worked out a base install to play with. Finally joined this wonderful community here and now I am ready to crank.

my first question is: in looking thru upgrade.php, i noticed that I will could use get_site_option to modify some default blog values. whats the appropriate folder/file to do drop a "add_site_option($key, $value)" ? if this was a per theme setting I would put it in themefolder/functions.php, but I need it to be made available regardless of which theme the main site or subsite is using.

THANKS in advance!